diff --git a/dev/objects.inv b/dev/objects.inv index b2c4e450..964c540a 100644 Binary files a/dev/objects.inv and b/dev/objects.inv differ diff --git a/dev/scripts/recon_surf.html b/dev/scripts/recon_surf.html index 28884b73..d38c4728 100644 --- a/dev/scripts/recon_surf.html +++ b/dev/scripts/recon_surf.html @@ -491,136 +491,6 @@

Usage If you use this for research publications, please cite: -Henschel L, Conjeti S, Estrada S, Diers K, Fischl B, Reuter M, FastSurfer - A - fast and accurate deep learning based neuroimaging pipeline, NeuroImage 219 - (2020), 117012. https://doi.org/10.1016/j.neuroimage.2020.117012 - -Henschel L*, Kuegler D*, Reuter M. (*co-first). FastSurferVINN: Building - Resolution-Independence into Deep Learning Segmentation Methods - A Solution - for HighRes Brain MRI. NeuroImage 251 (2022), 118933. - http://dx.doi.org/10.1016/j.neuroimage.2022.118933 - - -
-

Required arguments

- -
-
-

Optional arguments

- -
-
-

Other

- -
-
-

More parameters details

-

The --help flag of recon-surf.sh also prints details to your specific version of recon-surf.sh to the console.

-
$ ./recon-surf.sh --help
-
-Usage: recon-surf.sh --sid <sid> --sd <sdir> --t1 <t1> --asegdkt_segfile <asegdkt_segfile> [OPTIONS]
-
-recon-surf.sh takes a segmentation and T1 full head image and creates surfaces,
-thickness etc as a FS subject dir.
-
-FLAGS:
-  --sid <subjectID>       Subject ID to create directory inside $SUBJECTS_DIR 
-  --sd  <subjects_dir>    Output directory $SUBJECTS_DIR (or pass via env var)
-  --t1  <T1_input>        T1 full head input (not bias corrected). This must be
-                            a conformed image (dimensions: 256x256x256, voxel
-                            size: 1x1x1, LIA orientation, and data type UCHAR).
-                            Images can be conformed using FastSurferCNN's
-                            conform.py script (usage example: python3
-                            FastSurferCNN/data_loader/conform.py -i <T1_input>
-                            -o <conformed_T1_output>). Requires an ABSOLUTE Path!
-  --asegdkt_segfile <asegdkt_segfile>
-                          Name of intermediate DL-based segmentation file
-                            (similar to aparc+aseg). This must be conformed
-                            (voxel size: isotropic, LIA orientation, and, if voxel
-                            size 1mm, dimensions: 256x256x256). FastSurferCNN's
-                            segmentations are conformed by default; please ensure
-                            that segmentations produced otherwise are conformed.
-                            Requires an ABSOLUTE Path! Default location:
-                            $SUBJECTS_DIR/$sid/mri/aparc.DKTatlas+aseg.deep.mgz
-  --mask_name <mask_file> Path to the brain mask file to use. Default location:
-                            $SUBJECTS_DIR/$sid/mri/mask.mgz
-  --edits                 Disable the check for existing recon-surf.sh run, replace
-                            <asegdkt_segfile> by its manedit-suffixed version,
-                            includes wm.mgz and brain.finalsurfs.mgz edits,
-                            and enables FreeSurfer-style WM control points.
-  --fstess                Revert to FreeSurfer mri_tesselate for surface creation
-                            (default: mri_mc)
-  --fsqsphere             Revert to FreeSurfer iterative inflation for qsphere
-                            (default: spectral spherical projection)
-  --fsaparc               Additionally create FS aparc segmentations and ribbon.
-                            Skipped by default (--> DL prediction is used which
-                            is faster, and usually these mapped ones are fine).
-                            Note, if you switch this on it will create all cortical
-                            parcellations with FreeSurfer's spherical atlases and
-                            also map these into the aparc+aseg file instead of
-                            the FastSurfer ones. FastSurfer's cortical DKT atlas
-                            results can still be found in:
-                            <hemi>.aparc.DKTatlas.mapped.stats
-  --3T                    Use the 3T atlas for talairach registration (gives better
-                            eTIV estimates for 3T MR images, default: 1.5T atlas).
-  --threads <int>         Set openMP and ITK threads to <int>, parallelize
-                            hemispheres, if threads >= 2.
-  --py <python_cmd>       Command for python, default python3.10
-  --fs_license <license>  Path to FreeSurfer license key file. Register at
-                            https://surfer.nmr.mgh.harvard.edu/registration.html
-                            for free to obtain it if you do not have FreeSurfer
-                            installed already.
-  --base                  For longitudinal template (base) creation.
-  --long <baseid>         For longitudinal time point creation, pass the ID of
-                            the base (template) which needs to exist already in
-                            the same subjects_dir.
-  -h --help               Print Help
-
-Dev Flags:
-  --ignore_fs_version     Switch on to avoid check for FreeSurfer version.
-                            Program will otherwise terminate if 7.4.1 is 
-                            not sourced. Can be used for testing dev versions.
-  --no_fs_T1              Do not generate T1.mgz (normalized nu.mgz included in
-                            standard FreeSurfer output) and create brainmask.mgz
-                            directly from norm.mgz instead. Saves 1:30 min.
-  --no_surfreg            Do not run Surface registration with FreeSurfer (for
-                            cross-subject correspondence). Not recommended, but
-                            speeds up processing if you just need the stats and
-                            don't want to do thickness analysis on the cortex.
-
-REFERENCES:
-
-If you use this for research publications, please cite:
-
 Henschel L, Conjeti S, Estrada S, Diers K, Fischl B, Reuter M, FastSurfer - A
  fast and accurate deep learning based neuroimaging pipeline, NeuroImage 219
  (2020), 117012. https://doi.org/10.1016/j.neuroimage.2020.117012
@@ -632,7 +502,6 @@ 
More parameters details
-

Examples

@@ -822,13 +691,7 @@

Example 4: recon-surf on multiple subjectsSurface pipeline: recon-surf.sh
  • Overview
    • -
  • Usage -
    • +
  • Usage
  • Examples
    • Example 1: Surface module inside Docker
    • Example 2: recon-surf inside Singularity
        diff --git a/dev/searchindex.js b/dev/searchindex.js index 02b5fae7..5f4b9734 100644 --- a/dev/searchindex.js +++ b/dev/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"1. Dependency packages": [[89, "dependency-packages"]], "1. System Packages": [[89, "system-packages"]], "2. Conda for python": [[89, "conda-for-python"]], "2. Python": [[89, "python"]], "3. FastSurfer": [[89, "fastsurfer"]], "3. FastSurfer and Requirements": [[89, "fastsurfer-and-requirements"]], "4. Apple AI Accelerator support": [[89, "apple-ai-accelerator-support"]], "4. Python environment": [[89, "python-environment"]], "5. FreeSurfer": [[89, "freesurfer"]], "AMD GPUs (experimental)": [[89, "amd-gpus-experimental"]], "Acknowledgements": [[83, "acknowledgements"], [96, "acknowledgements"]], "Advanced Docker Flags": [[94, "advanced-docker-flags"]], "Advanced options": [[102, "CerebNet.run_prediction-setup_options-advanced-options"], [107, "HypVINN.run_prediction-option_parse-advanced-options"]], "Advanced options (not shown in -h)": [[111, "FastSurferCNN.segstats-make_arguments-advanced-options-(not-shown-in--h)"]], "Advanced scripts": [[101, null]], "Apache License": [[97, "apache-license"]], "Attribution": [[84, "attribution"], [85, "attribution"]], "BATCH: brun_fastsurfer.sh": [[99, null]], "Before Submitting a Bug Report": [[85, "before-submitting-a-bug-report"]], "Before Submitting an Enhancement": [[85, "before-submitting-an-enhancement"]], "Behind the Scenes:": [[90, "behind-the-scenes"]], "Bias field correction": [[86, "bias-field-correction"]], "Build docker image with attestation and provenance": [[94, "build-docker-image-with-attestation-and-provenance"]], "BuildKit": [[94, "buildkit"]], "Building your own FastSurfer Singularity Image": [[98, "building-your-own-fastsurfer-singularity-image"]], "CFG-file with default options for network": [[107, "cfg-file-with-default-options-for-network"]], "CerebNet": [[0, null]], "CerebNet.apply_warp": [[13, null]], "CerebNet.data_loader.augmentation": [[14, null]], "CerebNet.data_loader.data_utils": [[15, null]], "CerebNet.data_loader.dataset": [[16, null]], "CerebNet.data_loader.loader": [[17, null]], "CerebNet.dataloader": [[1, null]], "CerebNet.datasets": [[2, null]], "CerebNet.datasets.generate_hdf5": [[18, null]], "CerebNet.datasets.load_data": [[19, null]], "CerebNet.datasets.utils": [[20, null]], "CerebNet.datasets.wm_merge_clean": [[21, null]], "CerebNet.inference": [[22, null]], "CerebNet.models.networks": [[23, null]], "CerebNet.models.sub_module": [[24, null]], "CerebNet.run_prediction": [[25, null]], "CerebNet.utils": [[4, null]], "CerebNet.utils.checkpoint": [[26, null]], "CerebNet.utils.load_config": [[27, null]], "CerebNet.utils.lr_scheduler": [[28, null]], "CerebNet.utils.meters": [[29, null]], "CerebNet.utils.metrics": [[30, null]], "CerebNet.utils.misc": [[31, null]], "CerebNet: run_prediction.py": [[102, null]], "CerebNet_models": [[3, null]], "Cerebnet module": [[91, "cerebnet-module"]], "Checkpoint to load": [[107, "checkpoint-to-load"]], "Checkpoints and configs": [[103, "checkpoints-and-configs"]], "Citation": [[107, "citation"]], "Contributing Code": [[85, "contributing-code"]], "Contributing to FastSurfer": [[85, null]], "Contributor Covenant Code of Conduct": [[84, null]], "Data options": [[106, "data-options"]], "Debugging SLURM runs": [[100, "debugging-slurm-runs"]], "Developer": [[107, "developer"]], "Docker": [[87, "docker"], [89, "docker"]], "Docker (CPU version)": [[89, "docker-cpu-version"]], "Docker (GPU version)": [[89, "docker-gpu-version"]], "Docker (currently only supported for Intel CPUs)": [[89, "docker-currently-only-supported-for-intel-cpus"]], "Docker Best Practice": [[94, "docker-best-practice"]], "Docker Flags": [[94, "docker-flags"]], "Docker Support": [[94, null]], "Dual parallel pipeline": [[99, "dual-parallel-pipeline"]], "Enforcement": [[84, "enforcement"]], "Example 1: Build GPU FastSurfer Image": [[94, "example-1-build-gpu-fastsurfer-image"]], "Example 1: FastSurfer Docker": [[87, "example-1-fastsurfer-docker"]], "Example 1: Surface module inside Docker": [[110, "example-1-surface-module-inside-docker"]], "Example 2: Build CPU FastSurfer Image": [[94, "example-2-build-cpu-fastsurfer-image"]], "Example 2: FastSurfer Singularity": [[87, "example-2-fastsurfer-singularity"]], "Example 2: recon-surf inside Singularity": [[110, "example-2-recon-surf-inside-singularity"]], "Example 3: Experimental Build for AMD GPUs": [[94, "example-3-experimental-build-for-amd-gpus"]], "Example 3: Native FastSurfer on subjectX with parallel processing of hemis": [[87, "example-3-native-fastsurfer-on-subjectx-with-parallel-processing-of-hemis"]], "Example 3: Native installation - recon-surf on a single subject (subjectX)": [[110, "example-3-native-installation-recon-surf-on-a-single-subject-subjectx"]], "Example 4: FastSurfer on multiple subjects": [[87, "example-4-fastsurfer-on-multiple-subjects"]], "Example 4: recon-surf on multiple subjects": [[110, "example-4-recon-surf-on-multiple-subjects"]], "Example 5: Quick Segmentation": [[87, "example-5-quick-segmentation"]], "Example 6: Running FastSurfer on a SLURM cluster via Singularity": [[87, "example-6-running-fastsurfer-on-a-slurm-cluster-via-singularity"]], "Example Command: Evaluation Single Subject": [[103, "example-command-evaluation-single-subject"]], "Example Command: Evaluation whole directory": [[103, "example-command-evaluation-whole-directory"]], "Example Command: Training Default FastSurferVINN": [[106, "example-command-training-default-fastsurfervinn"]], "Example Command: Training FastSurferCNN": [[106, "example-command-training-fastsurfercnn"]], "Example Command: Training FastSurferVINN (Single Resolution)": [[106, "example-command-training-fastsurfervinn-single-resolution"]], "Examples": [[87, null], [110, "examples"]], "Expert usage": [[96, "expert-usage"]], "FastSurfer API": [[81, null]], "FastSurfer Docker Image Creation": [[94, "fastsurfer-docker-image-creation"]], "FastSurfer Flags": [[87, "fastsurfer-flags"], [88, null], [94, "fastsurfer-flags"], [98, "fastsurfer-flags"]], "FastSurfer License": [[97, null]], "FastSurfer Singularity Image Usage": [[98, "fastsurfer-singularity-image-usage"]], "FastSurfer Technical parameters (see FastSurfer documentation)": [[107, "fastsurfer-technical-parameters-see-fastsurfer-documentation"]], "FastSurfer Utilities": [[112, null]], "FastSurferCNN": [[5, null]], "FastSurferCNN.data_loader": [[6, null]], "FastSurferCNN.data_loader.augmentation": [[32, null]], "FastSurferCNN.data_loader.conform": [[33, null]], "FastSurferCNN.data_loader.data_utils": [[34, null]], "FastSurferCNN.data_loader.dataset": [[35, null]], "FastSurferCNN.data_loader.loader": [[36, null]], "FastSurferCNN.download_checkpoints": [[37, null]], "FastSurferCNN.generate_hdf5": [[38, null]], "FastSurferCNN.inference": [[39, null]], "FastSurferCNN.models": [[7, null]], "FastSurferCNN.models.interpolation_layer": [[40, null]], "FastSurferCNN.models.losses": [[41, null]], "FastSurferCNN.models.networks": [[42, null]], "FastSurferCNN.models.sub_module": [[43, null]], "FastSurferCNN.quick_qc": [[44, null]], "FastSurferCNN.reduce_to_aseg": [[45, null]], "FastSurferCNN.run_prediction": [[46, null]], "FastSurferCNN.segstats": [[47, null]], "FastSurferCNN.utils": [[8, null]], "FastSurferCNN.utils.arg_types": [[48, null]], "FastSurferCNN.utils.checkpoint": [[49, null]], "FastSurferCNN.utils.common": [[50, null]], "FastSurferCNN.utils.load_config": [[51, null]], "FastSurferCNN.utils.logging": [[52, null]], "FastSurferCNN.utils.lr_scheduler": [[53, null]], "FastSurferCNN.utils.mapper": [[54, null]], "FastSurferCNN.utils.meters": [[55, null]], "FastSurferCNN.utils.metrics": [[56, null]], "FastSurferCNN.utils.misc": [[57, null]], "FastSurferCNN.utils.parser_defaults": [[58, null]], "FastSurferCNN.utils.run_tools": [[59, null]], "FastSurferCNN.utils.threads": [[60, null]], "FastSurferCNN.version": [[61, null]], "FastSurferCNN: download_checkpoints.py": [[104, null]], "FastSurferCNN: generate_hdf5.py": [[105, null]], "FastSurferCNN: run_model.py": [[106, null]], "FastSurferCNN: run_prediction.py": [[103, null]], "FastSurferCNN: segstats.py": [[111, null]], "Final Statistics:": [[90, "final-statistics"]], "Flags": [[87, "flags"]], "FreeSurfer Downstream Modules": [[96, "freesurfer-downstream-modules"]], "Full commandline interface of FastSurferCNN/download_checkpoints.py": [[104, "full-commandline-interface-of-fastsurfercnn-download-checkpoints-py"]], "Full commandline interface of FastSurferCNN/generate_hdf5.py": [[105, "full-commandline-interface-of-fastsurfercnn-generate-hdf5-py"]], "Full commandline interface of FastSurferCNN/run_model.py": [[106, "full-commandline-interface-of-fastsurfercnn-run-model-py"]], "Full commandline interface of FastSurferCNN/run_prediction.py": [[103, "full-commandline-interface-of-fastsurfercnn-run-prediction-py"]], "Full commandline interface of FastSurferCNN/segstats.py": [[111, "full-commandline-interface-of-fastsurfercnn-segstats-py"]], "Full list of flags": [[88, "full-list-of-flags"]], "General": [[103, "general"]], "General build settings": [[94, "general-build-settings"]], "General process": [[86, "general-process"]], "Google Colab": [[92, "google-colab"]], "Guide for experienced FreeSurfer users": [[86, "guide-for-experienced-freesurfer-users"]], "How Do I Submit a Good Bug Report?": [[85, "how-do-i-submit-a-good-bug-report"]], "How Do I Submit a Good Enhancement Suggestion?": [[85, "how-do-i-submit-a-good-enhancement-suggestion"]], "How to Run Your Data": [[90, "how-to-run-your-data"]], "HypVINN": [[9, null]], "HypVINN module": [[91, "hypvinn-module"]], "HypVINN.data_loader": [[10, null]], "HypVINN.data_loader.data_utils": [[62, null]], "HypVINN.data_loader.dataset": [[63, null]], "HypVINN.inference": [[64, null]], "HypVINN.models": [[11, null]], "HypVINN.models.networks": [[65, null]], "HypVINN.run_prediction": [[66, null]], "HypVINN.utils": [[12, null]], "HypVINN: run_prediction.py": [[107, null]], "Image processing options": [[107, "image-processing-options"]], "Input": [[107, "input"]], "Input and output arguments": [[107, "input-and-output-arguments"]], "Installation": [[89, null]], "Intended Use": [[96, "intended-use"]], "Introduction to FastSurfer": [[96, null]], "LONG: long_fastsurfer.sh": [[109, null]], "Linux": [[89, "linux"]], "Longitudinal Processing": [[90, null]], "MacOS": [[89, "macos"]], "Manual Edits": [[86, null]], "Minimum Requirements:": [[96, "minimum-requirements"]], "Misc. Options": [[106, "misc-options"]], "Model options": [[106, "model-options"]], "Model weights": [[107, "model-weights"]], "More parameters details": [[110, "more-parameters-details"]], "Mounting Home": [[98, "mounting-home"]], "Named Arguments": [[102, "CerebNet.run_prediction-setup_options-named-arguments"], [103, "FastSurferCNN.run_prediction-make_parser-named-arguments"], [104, "FastSurferCNN.download_checkpoints-make_parser-named-arguments"], [105, "FastSurferCNN.generate_hdf5-make_parser-named-arguments"], [106, "FastSurferCNN.run_model-make_parser-named-arguments"], [107, "HypVINN.run_prediction-option_parse-named-arguments"], [111, "FastSurferCNN.segstats-make_arguments-named-arguments"], [111, "named-arguments"]], "Native": [[87, "native"], [89, "native"]], "Native (Ubuntu 20.04 or Ubuntu 22.04)": [[89, "native-ubuntu-20-04-or-ubuntu-22-04"]], "Notebook 1 - Quick and Easy - FastSurfer Segmentation with three clicks": [[92, "notebook-1-quick-and-easy-fastsurfer-segmentation-with-three-clicks"]], "Notebook 2 - Complete FastSurfer Tutorial": [[92, "notebook-2-complete-fastsurfer-tutorial"]], "Optimizer options": [[106, "optimizer-options"]], "Optional arguments": [[110, "optional-arguments"]], "Optional commands": [[103, "optional-commands"]], "Other": [[110, "other"]], "Our Pledge": [[84, "our-pledge"]], "Our Responsibilities": [[84, "our-responsibilities"]], "Our Standards": [[84, "our-standards"]], "Output": [[107, "output"]], "Output files": [[91, null]], "Overview": [[83, "overview"], [110, "overview"]], "Parallelization with brun_fastsurfer.sh": [[99, "parallelization-with-brun-fastsurfer-sh"]], "Pial surface placement": [[86, "pial-surface-placement"]], "Pipeline Steps": [[107, "pipeline-steps"]], "Pipeline overview": [[86, "pipeline-overview"]], "Positional Arguments": [[102, "CerebNet.run_prediction-setup_options-positional-arguments"], [104, "FastSurferCNN.download_checkpoints-make_parser-positional-arguments"], [106, "FastSurferCNN.run_model-make_parser-positional-arguments"]], "Possible Edits": [[86, "possible-edits"]], "Pull FastSurfer from DockerHub": [[94, "pull-fastsurfer-from-dockerhub"]], "Questions": [[99, "questions"]], "Quick Start": [[92, null]], "References": [[83, "references"], [90, "references"], [96, "references"]], "Reporting Bugs": [[85, "reporting-bugs"]], "Reporting a Vulnerability": [[93, "reporting-a-vulnerability"]], "Required arguments": [[88, "required-arguments"], [110, "required-arguments"]], "Required for Docker when running surface module": [[88, "required-for-docker-when-running-surface-module"]], "Requirements": [[107, "requirements"]], "Running the official Docker Image": [[94, "running-the-official-docker-image"]], "Running the tool": [[107, "running-the-tool"]], "SLURM: srun_fastsurfer.sh": [[100, null]], "Scope": [[84, "scope"]], "Scripts": [[108, null]], "Security Policy": [[93, null]], "See Also": [[46, "see-also"]], "Segmentation Modules": [[83, "segmentation-modules"]], "Segmentation module": [[91, "segmentation-module"]], "Segmentation pipeline arguments (optional)": [[88, "segmentation-pipeline-arguments-optional"]], "Serial processing (default)": [[99, "serial-processing-default"]], "Side effects of edits": [[86, "side-effects-of-edits"]], "Single parallel pipeline": [[99, "single-parallel-pipeline"]], "Singularity": [[87, "singularity"], [89, "singularity"]], "Singularity Best Practice": [[98, "singularity-best-practice"]], "Singularity Flags": [[87, "singularity-flags"], [98, "singularity-flags"]], "Singularity Flags:": [[110, "singularity-flags"]], "Singularity Support": [[98, null]], "Singularity or Docker": [[92, "singularity-or-docker"]], "Singularity with the official FastSurfer Image": [[98, "singularity-with-the-official-fastsurfer-image"]], "Singularity without a GPU": [[98, "singularity-without-a-gpu"]], "Some other flags (optional)": [[88, "some-other-flags-optional"]], "Sub-commands": [[111, "Sub-commands"]], "Subject Lists": [[99, "subject-lists"]], "Suboptions": [[111, "FastSurferCNN.segstats-make_arguments-suboptions"]], "Suggesting Enhancements": [[85, "suggesting-enhancements"]], "Supported Versions": [[93, "supported-versions"]], "Surface module": [[91, "surface-module"]], "Surface pipeline arguments (optional)": [[88, "surface-pipeline-arguments-optional"]], "Surface pipeline: recon-surf.sh": [[110, null]], "Surface reconstruction": [[83, "surface-reconstruction"]], "System Requirements": [[96, "system-requirements"]], "Talairach registration": [[86, "talairach-registration"]], "Training options": [[106, "training-options"]], "Usage": [[99, "usage"], [100, "usage"], [107, "usage"], [110, "usage"]], "Usage help text": [[109, "usage-help-text"]], "User Guide": [[95, null]], "Welcome to FastSurfer!": [[83, null]], "What NOT to do": [[86, "what-not-to-do"]], "What are Edits?": [[86, "what-are-edits"]], "What can be edited?": [[86, "what-can-be-edited"]], "What is Longitudinal Processing": [[90, "what-is-longitudinal-processing"]], "What to do": [[86, "what-to-do"], [86, "id2"], [86, "id4"], [86, "id6"], [86, "id8"]], "When to use": [[86, "when-to-use"], [86, "id1"], [86, "id3"], [86, "id5"], [86, "id7"]], "White matter segmentation": [[86, "white-matter-segmentation"]], "Windows": [[89, "windows"]], "asegdkt_segfile": [[86, "asegdkt-segfile"]], "measures": [[111, "measures"]], "recon_surf": [[82, null]], "recon_surf.N4_bias_correct": [[67, null]], "recon_surf.align_points": [[68, null]], "recon_surf.align_seg": [[69, null]], "recon_surf.create_annotation": [[70, null]], "recon_surf.fs_balabels": [[71, null]], "recon_surf.lta": [[72, null]], "recon_surf.map_surf_label": [[73, null]], "recon_surf.paint_cc_into_pred": [[74, null]], "recon_surf.rewrite_mc_surface": [[75, null]], "recon_surf.rewrite_oriented_surface": [[76, null]], "recon_surf.rotate_sphere": [[77, null]], "recon_surf.sample_parc": [[78, null]], "recon_surf.smooth_aparc": [[79, null]], "recon_surf.spherically_project_wrapper": [[80, null]]}, "docnames": ["api/CerebNet", "api/CerebNet_dataloader", "api/CerebNet_datasets", "api/CerebNet_models", "api/CerebNet_utils", "api/FastSurferCNN", "api/FastSurferCNN.data_loader", "api/FastSurferCNN.models", "api/FastSurferCNN.utils", "api/HypVINN", "api/HypVINN_dataloader", "api/HypVINN_models", "api/HypVINN_utils", "api/generated/CerebNet.apply_warp", "api/generated/CerebNet.data_loader.augmentation", "api/generated/CerebNet.data_loader.data_utils", "api/generated/CerebNet.data_loader.dataset", "api/generated/CerebNet.data_loader.loader", "api/generated/CerebNet.datasets.generate_hdf5", "api/generated/CerebNet.datasets.load_data", "api/generated/CerebNet.datasets.utils", "api/generated/CerebNet.datasets.wm_merge_clean", "api/generated/CerebNet.inference", "api/generated/CerebNet.models.networks", "api/generated/CerebNet.models.sub_module", "api/generated/CerebNet.run_prediction", "api/generated/CerebNet.utils.checkpoint", "api/generated/CerebNet.utils.load_config", "api/generated/CerebNet.utils.lr_scheduler", "api/generated/CerebNet.utils.meters", "api/generated/CerebNet.utils.metrics", "api/generated/CerebNet.utils.misc", "api/generated/FastSurferCNN.data_loader.augmentation", "api/generated/FastSurferCNN.data_loader.conform", "api/generated/FastSurferCNN.data_loader.data_utils", "api/generated/FastSurferCNN.data_loader.dataset", "api/generated/FastSurferCNN.data_loader.loader", "api/generated/FastSurferCNN.download_checkpoints", "api/generated/FastSurferCNN.generate_hdf5", "api/generated/FastSurferCNN.inference", "api/generated/FastSurferCNN.models.interpolation_layer", "api/generated/FastSurferCNN.models.losses", "api/generated/FastSurferCNN.models.networks", "api/generated/FastSurferCNN.models.sub_module", "api/generated/FastSurferCNN.quick_qc", "api/generated/FastSurferCNN.reduce_to_aseg", "api/generated/FastSurferCNN.run_prediction", "api/generated/FastSurferCNN.segstats", "api/generated/FastSurferCNN.utils.arg_types", "api/generated/FastSurferCNN.utils.checkpoint", "api/generated/FastSurferCNN.utils.common", "api/generated/FastSurferCNN.utils.load_config", "api/generated/FastSurferCNN.utils.logging", "api/generated/FastSurferCNN.utils.lr_scheduler", "api/generated/FastSurferCNN.utils.mapper", "api/generated/FastSurferCNN.utils.meters", "api/generated/FastSurferCNN.utils.metrics", "api/generated/FastSurferCNN.utils.misc", "api/generated/FastSurferCNN.utils.parser_defaults", "api/generated/FastSurferCNN.utils.run_tools", "api/generated/FastSurferCNN.utils.threads", "api/generated/FastSurferCNN.version", "api/generated/HypVINN.data_loader.data_utils", "api/generated/HypVINN.data_loader.dataset", "api/generated/HypVINN.inference", "api/generated/HypVINN.models.networks", "api/generated/HypVINN.run_prediction", "api/generated/recon_surf.N4_bias_correct", "api/generated/recon_surf.align_points", "api/generated/recon_surf.align_seg", "api/generated/recon_surf.create_annotation", "api/generated/recon_surf.fs_balabels", "api/generated/recon_surf.lta", "api/generated/recon_surf.map_surf_label", "api/generated/recon_surf.paint_cc_into_pred", "api/generated/recon_surf.rewrite_mc_surface", "api/generated/recon_surf.rewrite_oriented_surface", "api/generated/recon_surf.rotate_sphere", "api/generated/recon_surf.sample_parc", "api/generated/recon_surf.smooth_aparc", "api/generated/recon_surf.spherically_project_wrapper", "api/index", "api/recon_surf", "index", "overview/CODE_OF_CONDUCT", "overview/CONTRIBUTING", "overview/EDITING", "overview/EXAMPLES", "overview/FLAGS", "overview/INSTALL", "overview/LONG", "overview/OUTPUT_FILES", "overview/QUICKSTART", "overview/SECURITY", "overview/docker", "overview/index", "overview/intro", "overview/license", "overview/singularity", "scripts/BATCH", "scripts/SLURM", "scripts/advanced", "scripts/cerebnet", "scripts/fastsurfercnn", "scripts/fastsurfercnn.download_checkpoints", "scripts/fastsurfercnn.generate_hdf5", "scripts/fastsurfercnn.run_model", "scripts/hypvinn", "scripts/index", "scripts/long_fastsurfer", "scripts/recon_surf", "scripts/segstats", "scripts/util"], "envversion": {"sphinx": 62, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinxcontrib.bibtex": 9}, "filenames": ["api/CerebNet.rst", "api/CerebNet_dataloader.rst", "api/CerebNet_datasets.rst", "api/CerebNet_models.rst", "api/CerebNet_utils.rst", "api/FastSurferCNN.rst", "api/FastSurferCNN.data_loader.rst", "api/FastSurferCNN.models.rst", "api/FastSurferCNN.utils.rst", "api/HypVINN.rst", "api/HypVINN_dataloader.rst", "api/HypVINN_models.rst", "api/HypVINN_utils.rst", "api/generated/CerebNet.apply_warp.rst", "api/generated/CerebNet.data_loader.augmentation.rst", "api/generated/CerebNet.data_loader.data_utils.rst", "api/generated/CerebNet.data_loader.dataset.rst", "api/generated/CerebNet.data_loader.loader.rst", "api/generated/CerebNet.datasets.generate_hdf5.rst", "api/generated/CerebNet.datasets.load_data.rst", "api/generated/CerebNet.datasets.utils.rst", "api/generated/CerebNet.datasets.wm_merge_clean.rst", "api/generated/CerebNet.inference.rst", "api/generated/CerebNet.models.networks.rst", "api/generated/CerebNet.models.sub_module.rst", "api/generated/CerebNet.run_prediction.rst", "api/generated/CerebNet.utils.checkpoint.rst", "api/generated/CerebNet.utils.load_config.rst", "api/generated/CerebNet.utils.lr_scheduler.rst", "api/generated/CerebNet.utils.meters.rst", "api/generated/CerebNet.utils.metrics.rst", "api/generated/CerebNet.utils.misc.rst", "api/generated/FastSurferCNN.data_loader.augmentation.rst", "api/generated/FastSurferCNN.data_loader.conform.rst", "api/generated/FastSurferCNN.data_loader.data_utils.rst", "api/generated/FastSurferCNN.data_loader.dataset.rst", "api/generated/FastSurferCNN.data_loader.loader.rst", "api/generated/FastSurferCNN.download_checkpoints.rst", "api/generated/FastSurferCNN.generate_hdf5.rst", "api/generated/FastSurferCNN.inference.rst", "api/generated/FastSurferCNN.models.interpolation_layer.rst", "api/generated/FastSurferCNN.models.losses.rst", "api/generated/FastSurferCNN.models.networks.rst", "api/generated/FastSurferCNN.models.sub_module.rst", "api/generated/FastSurferCNN.quick_qc.rst", "api/generated/FastSurferCNN.reduce_to_aseg.rst", "api/generated/FastSurferCNN.run_prediction.rst", "api/generated/FastSurferCNN.segstats.rst", "api/generated/FastSurferCNN.utils.arg_types.rst", "api/generated/FastSurferCNN.utils.checkpoint.rst", "api/generated/FastSurferCNN.utils.common.rst", "api/generated/FastSurferCNN.utils.load_config.rst", "api/generated/FastSurferCNN.utils.logging.rst", "api/generated/FastSurferCNN.utils.lr_scheduler.rst", "api/generated/FastSurferCNN.utils.mapper.rst", "api/generated/FastSurferCNN.utils.meters.rst", "api/generated/FastSurferCNN.utils.metrics.rst", "api/generated/FastSurferCNN.utils.misc.rst", "api/generated/FastSurferCNN.utils.parser_defaults.rst", "api/generated/FastSurferCNN.utils.run_tools.rst", "api/generated/FastSurferCNN.utils.threads.rst", "api/generated/FastSurferCNN.version.rst", "api/generated/HypVINN.data_loader.data_utils.rst", "api/generated/HypVINN.data_loader.dataset.rst", "api/generated/HypVINN.inference.rst", "api/generated/HypVINN.models.networks.rst", "api/generated/HypVINN.run_prediction.rst", "api/generated/recon_surf.N4_bias_correct.rst", "api/generated/recon_surf.align_points.rst", "api/generated/recon_surf.align_seg.rst", "api/generated/recon_surf.create_annotation.rst", "api/generated/recon_surf.fs_balabels.rst", "api/generated/recon_surf.lta.rst", "api/generated/recon_surf.map_surf_label.rst", "api/generated/recon_surf.paint_cc_into_pred.rst", "api/generated/recon_surf.rewrite_mc_surface.rst", "api/generated/recon_surf.rewrite_oriented_surface.rst", "api/generated/recon_surf.rotate_sphere.rst", "api/generated/recon_surf.sample_parc.rst", "api/generated/recon_surf.smooth_aparc.rst", "api/generated/recon_surf.spherically_project_wrapper.rst", "api/index.rst", "api/recon_surf.rst", "index.rst", "overview/CODE_OF_CONDUCT.md", "overview/CONTRIBUTING.md", "overview/EDITING.md", "overview/EXAMPLES.md", "overview/FLAGS.md", "overview/INSTALL.md", "overview/LONG.md", "overview/OUTPUT_FILES.md", "overview/QUICKSTART.md", "overview/SECURITY.md", "overview/docker.rst", "overview/index.rst", "overview/intro.rst", "overview/license.rst", "overview/singularity.rst", "scripts/BATCH.md", "scripts/SLURM.md", "scripts/advanced.rst", "scripts/cerebnet.rst", "scripts/fastsurfercnn.rst", "scripts/fastsurfercnn.download_checkpoints.rst", "scripts/fastsurfercnn.generate_hdf5.rst", "scripts/fastsurfercnn.run_model.rst", "scripts/hypvinn.rst", "scripts/index.rst", "scripts/long_fastsurfer.rst", "scripts/recon_surf.rst", "scripts/segstats.rst", "scripts/util.rst"], "indexentries": {"add_argument() (fastsurfercnn.utils.parser_defaults.canaddarguments method)": [[58, "FastSurferCNN.utils.parser_defaults.CanAddArguments.add_argument", false]], "add_arguments() (in module fastsurfercnn.utils.parser_defaults)": [[58, "FastSurferCNN.utils.parser_defaults.add_arguments", false]], "add_cereb_wm() (in module cerebnet.datasets.wm_merge_clean)": [[21, "CerebNet.datasets.wm_merge_clean.add_cereb_wm", false]], "add_measure_parser() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.add_measure_parser", false]], "add_plane_flags() (in module fastsurfercnn.utils.parser_defaults)": [[58, "FastSurferCNN.utils.parser_defaults.add_plane_flags", false]], "add_two_help_messages() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.add_two_help_messages", false]], "addgaussiannoise (class in fastsurfercnn.data_loader.augmentation)": [[32, "FastSurferCNN.data_loader.augmentation.AddGaussianNoise", false]], "align_aparc_centroids() (in module recon_surf.rotate_sphere)": [[77, "recon_surf.rotate_sphere.align_aparc_centroids", false]], "align_flipped() (in module recon_surf.align_seg)": [[69, "recon_surf.align_seg.align_flipped", false]], "align_seg_centroids() (in module recon_surf.align_seg)": [[69, "recon_surf.align_seg.align_seg_centroids", false]], "angles2rmat() (in module recon_surf.align_points)": [[68, "recon_surf.align_points.angles2rmat", false]], "are_all_subject_files() (fastsurfercnn.utils.common.subjectlist method)": [[50, "FastSurferCNN.utils.common.SubjectList.are_all_subject_files", false]], "args2cfg() (in module fastsurfercnn.run_prediction)": [[46, "FastSurferCNN.run_prediction.args2cfg", false]], "argument_parse() (in module recon_surf.paint_cc_into_pred)": [[74, "recon_surf.paint_cc_into_pred.argument_parse", false]], "as_future() (fastsurfercnn.utils.run_tools.popen method)": [[59, "FastSurferCNN.utils.run_tools.Popen.as_future", false]], "asegdkt_segfile (fastsurfercnn.utils.common.subjectdirectory property)": [[50, "FastSurferCNN.utils.common.SubjectDirectory.asegdkt_segfile", false]], "assert_no_root() (in module fastsurfercnn.utils.common)": [[50, "FastSurferCNN.utils.common.assert_no_root", false]], "async_save_img() (fastsurfercnn.run_prediction.runmodelondata method)": [[46, "FastSurferCNN.run_prediction.RunModelOnData.async_save_img", false]], "augmentationpadimage (class in fastsurfercnn.data_loader.augmentation)": [[32, "FastSurferCNN.data_loader.augmentation.AugmentationPadImage", false]], "augmentationrandomcrop (class in fastsurfercnn.data_loader.augmentation)": [[32, "FastSurferCNN.data_loader.augmentation.AugmentationRandomCrop", false]], "bbox_3d() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.bbox_3d", false]], "bincount2d_vectorized() (in module recon_surf.smooth_aparc)": [[79, "recon_surf.smooth_aparc.bincount2D_vectorized", false]], "borders() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.borders", false]], "bounding_volume_offset() (in module cerebnet.datasets.utils)": [[20, "CerebNet.datasets.utils.bounding_volume_offset", false]], "build_annot() (in module recon_surf.create_annotation)": [[70, "recon_surf.create_annotation.build_annot", false]], "build_model() (in module cerebnet.models.networks)": [[23, "CerebNet.models.networks.build_model", false]], "build_model() (in module fastsurfercnn.models.networks)": [[42, "FastSurferCNN.models.networks.build_model", false]], "build_model() (in module hypvinn.models.networks)": [[65, "HypVINN.models.networks.build_model", false]], "calculate_flip_orientation() (in module hypvinn.data_loader.data_utils)": [[62, "HypVINN.data_loader.data_utils.calculate_flip_orientation", false]], "calculate_merged_labels() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.calculate_merged_labels", false]], "call() (in module recon_surf.spherically_project_wrapper)": [[80, "recon_surf.spherically_project_wrapper.call", false]], "can_resolve_attribute() (fastsurfercnn.utils.common.subjectdirectory method)": [[50, "FastSurferCNN.utils.common.SubjectDirectory.can_resolve_attribute", false]], "can_resolve_filename() (fastsurfercnn.utils.common.subjectdirectory method)": [[50, "FastSurferCNN.utils.common.SubjectDirectory.can_resolve_filename", false]], "canaddarguments (class in fastsurfercnn.utils.parser_defaults)": [[58, "FastSurferCNN.utils.parser_defaults.CanAddArguments", false]], "cereb_subseg_lateral_mask() (in module cerebnet.datasets.wm_merge_clean)": [[21, "CerebNet.datasets.wm_merge_clean.cereb_subseg_lateral_mask", false]], "cerebdataset (class in cerebnet.data_loader.dataset)": [[16, "CerebNet.data_loader.dataset.CerebDataset", false]], "cerebnet.apply_warp": [[13, "module-CerebNet.apply_warp", false]], "cerebnet.data_loader.augmentation": [[14, "module-CerebNet.data_loader.augmentation", false]], "cerebnet.data_loader.data_utils": [[15, "module-CerebNet.data_loader.data_utils", false]], "cerebnet.data_loader.dataset": [[16, "module-CerebNet.data_loader.dataset", false]], "cerebnet.data_loader.loader": [[17, "module-CerebNet.data_loader.loader", false]], "cerebnet.datasets.generate_hdf5": [[18, "module-CerebNet.datasets.generate_hdf5", false]], "cerebnet.datasets.load_data": [[19, "module-CerebNet.datasets.load_data", false]], "cerebnet.datasets.utils": [[20, "module-CerebNet.datasets.utils", false]], "cerebnet.datasets.wm_merge_clean": [[21, "module-CerebNet.datasets.wm_merge_clean", false]], "cerebnet.inference": [[22, "module-CerebNet.inference", false]], "cerebnet.models.networks": [[23, "module-CerebNet.models.networks", false]], "cerebnet.models.sub_module": [[24, "module-CerebNet.models.sub_module", false]], "cerebnet.run_prediction": [[25, "module-CerebNet.run_prediction", false]], "cerebnet.utils.checkpoint": [[26, "module-CerebNet.utils.checkpoint", false]], "cerebnet.utils.load_config": [[27, "module-CerebNet.utils.load_config", false]], "cerebnet.utils.lr_scheduler": [[28, "module-CerebNet.utils.lr_scheduler", false]], "cerebnet.utils.meters": [[29, "module-CerebNet.utils.meters", false]], "cerebnet.utils.metrics": [[30, "module-CerebNet.utils.metrics", false]], "cerebnet.utils.misc": [[31, "module-CerebNet.utils.misc", false]], "cerebnetdataset (class in cerebnet.datasets.generate_hdf5)": [[18, "CerebNet.datasets.generate_hdf5.CerebNetDataset", false]], "chain() (fastsurfercnn.utils.mapper.mapper method)": [[54, "FastSurferCNN.utils.mapper.Mapper.chain", false]], "check_affine_in_nifti() (in module fastsurfercnn.data_loader.conform)": [[33, "FastSurferCNN.data_loader.conform.check_affine_in_nifti", false]], "check_and_download_ckpts() (in module fastsurfercnn.utils.checkpoint)": [[49, "FastSurferCNN.utils.checkpoint.check_and_download_ckpts", false]], "check_path() (in module fastsurfercnn.utils.misc)": [[57, "FastSurferCNN.utils.misc.check_path", false]], "check_shape_affine() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.check_shape_affine", false]], "check_volume() (in module fastsurfercnn.quick_qc)": [[44, "FastSurferCNN.quick_qc.check_volume", false]], "checkpointconfigdict (class in fastsurfercnn.utils.checkpoint)": [[49, "FastSurferCNN.utils.checkpoint.CheckpointConfigDict", false]], "classes (fastsurfercnn.utils.mapper.colorlookuptable property)": [[54, "FastSurferCNN.utils.mapper.ColorLookupTable.classes", false]], "classifierblock (class in cerebnet.models.sub_module)": [[24, "CerebNet.models.sub_module.ClassifierBlock", false]], "classifierblock (class in fastsurfercnn.models.sub_module)": [[43, "FastSurferCNN.models.sub_module.ClassifierBlock", false]], "clean_cortex_labels() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.clean_cortex_labels", false]], "color_palette (fastsurfercnn.utils.mapper.colorlookuptable property)": [[54, "FastSurferCNN.utils.mapper.ColorLookupTable.color_palette", false]], "colorlookuptable (class in fastsurfercnn.utils.mapper)": [[54, "FastSurferCNN.utils.mapper.ColorLookupTable", false]], "colormap() (fastsurfercnn.utils.mapper.colorlookuptable method)": [[54, "FastSurferCNN.utils.mapper.ColorLookupTable.colormap", false]], "combinedloss (class in fastsurfercnn.models.losses)": [[41, "FastSurferCNN.models.losses.CombinedLoss", false]], "competitivedecoderblock (class in cerebnet.models.sub_module)": [[24, "CerebNet.models.sub_module.CompetitiveDecoderBlock", false]], "competitivedecoderblock (class in fastsurfercnn.models.sub_module)": [[43, "FastSurferCNN.models.sub_module.CompetitiveDecoderBlock", false]], "competitivedenseblock (class in cerebnet.models.sub_module)": [[24, "CerebNet.models.sub_module.CompetitiveDenseBlock", false]], "competitivedenseblock (class in fastsurfercnn.models.sub_module)": [[43, "FastSurferCNN.models.sub_module.CompetitiveDenseBlock", false]], "competitivedenseblockinput (class in cerebnet.models.sub_module)": [[24, "CerebNet.models.sub_module.CompetitiveDenseBlockInput", false]], "competitivedenseblockinput (class in fastsurfercnn.models.sub_module)": [[43, "FastSurferCNN.models.sub_module.CompetitiveDenseBlockInput", false]], "competitiveencoderblock (class in cerebnet.models.sub_module)": [[24, "CerebNet.models.sub_module.CompetitiveEncoderBlock", false]], "competitiveencoderblock (class in fastsurfercnn.models.sub_module)": [[43, "FastSurferCNN.models.sub_module.CompetitiveEncoderBlock", false]], "competitiveencoderblockinput (class in cerebnet.models.sub_module)": [[24, "CerebNet.models.sub_module.CompetitiveEncoderBlockInput", false]], "competitiveencoderblockinput (class in fastsurfercnn.models.sub_module)": [[43, "FastSurferCNN.models.sub_module.CompetitiveEncoderBlockInput", false]], "comput_dice_cnf() (fastsurfercnn.utils.metrics.dicescore method)": [[56, "FastSurferCNN.utils.metrics.DiceScore.comput_dice_cnf", false]], "compute() (cerebnet.utils.metrics.dicescore method)": [[30, "CerebNet.utils.metrics.DiceScore.compute", false]], "compute_dsc() (fastsurfercnn.utils.metrics.dicescore method)": [[56, "FastSurferCNN.utils.metrics.DiceScore.compute_dsc", false]], "conf_name (fastsurfercnn.utils.common.subjectdirectory property)": [[50, "FastSurferCNN.utils.common.SubjectDirectory.conf_name", false]], "conform() (in module fastsurfercnn.data_loader.conform)": [[33, "FastSurferCNN.data_loader.conform.conform", false]], "conform_and_save_orig() (fastsurfercnn.run_prediction.runmodelondata method)": [[46, "FastSurferCNN.run_prediction.RunModelOnData.conform_and_save_orig", false]], "construct_adj_cluster() (in module recon_surf.sample_parc)": [[78, "recon_surf.sample_parc.construct_adj_cluster", false]], "copy_orig_name (fastsurfercnn.utils.common.subjectdirectory property)": [[50, "FastSurferCNN.utils.common.SubjectDirectory.copy_orig_name", false]], "correct_cereb_brainstem() (in module cerebnet.datasets.wm_merge_clean)": [[21, "CerebNet.datasets.wm_merge_clean.correct_cereb_brainstem", false]], "cortex_border_mask() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.cortex_border_mask", false]], "cosineannealingwarmrestartsdecay (class in cerebnet.utils.lr_scheduler)": [[28, "CerebNet.utils.lr_scheduler.CosineAnnealingWarmRestartsDecay", false]], "cosinelr (class in cerebnet.utils.lr_scheduler)": [[28, "CerebNet.utils.lr_scheduler.CosineLR", false]], "create_annotation() (in module recon_surf.create_annotation)": [[70, "recon_surf.create_annotation.create_annotation", false]], "create_checkpoint_dir() (in module cerebnet.utils.checkpoint)": [[26, "CerebNet.utils.checkpoint.create_checkpoint_dir", false]], "create_checkpoint_dir() (in module fastsurfercnn.utils.checkpoint)": [[49, "FastSurferCNN.utils.checkpoint.create_checkpoint_dir", false]], "create_hdf5_dataset() (cerebnet.datasets.generate_hdf5.cerebnetdataset method)": [[18, "CerebNet.datasets.generate_hdf5.CerebNetDataset.create_hdf5_dataset", false]], "create_hdf5_dataset() (fastsurfercnn.generate_hdf5.h5pydataset method)": [[38, "FastSurferCNN.generate_hdf5.H5pyDataset.create_hdf5_dataset", false]], "create_mask() (in module fastsurfercnn.reduce_to_aseg)": [[45, "FastSurferCNN.reduce_to_aseg.create_mask", false]], "create_weight_mask() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.create_weight_mask", false]], "create_weight_mask2d() (in module cerebnet.data_loader.data_utils)": [[15, "CerebNet.data_loader.data_utils.create_weight_mask2d", false]], "criteria (class in fastsurfercnn.data_loader.conform)": [[33, "FastSurferCNN.data_loader.conform.Criteria", false]], "crop_patch_to_mask() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.crop_patch_to_mask", false]], "crop_position (fastsurfercnn.models.interpolation_layer.zoom2d property)": [[40, "FastSurferCNN.models.interpolation_layer.Zoom2d.crop_position", false]], "crop_position (fastsurfercnn.models.interpolation_layer.zoom3d property)": [[40, "FastSurferCNN.models.interpolation_layer.Zoom3d.crop_position", false]], "crop_transform() (in module cerebnet.datasets.utils)": [[20, "CerebNet.datasets.utils.crop_transform", false]], "crossentropy2d (class in fastsurfercnn.models.losses)": [[41, "FastSurferCNN.models.losses.CrossEntropy2D", false]], "dataframe() (fastsurfercnn.utils.mapper.jsoncolorlookuptable method)": [[54, "FastSurferCNN.utils.mapper.JsonColorLookupTable.dataframe", false]], "dataframe() (fastsurfercnn.utils.mapper.tsvlookuptable method)": [[54, "FastSurferCNN.utils.mapper.TSVLookupTable.dataframe", false]], "decay_base_lr() (cerebnet.utils.lr_scheduler.cosineannealingwarmrestartsdecay method)": [[28, "CerebNet.utils.lr_scheduler.CosineAnnealingWarmRestartsDecay.decay_base_lr", false]], "deep_sulci_and_wm_strand_mask() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.deep_sulci_and_wm_strand_mask", false]], "dice_score() (in module cerebnet.utils.metrics)": [[30, "CerebNet.utils.metrics.dice_score", false]], "dice_score() (in module fastsurfercnn.utils.metrics)": [[56, "FastSurferCNN.utils.metrics.dice_score", false]], "diceloss (class in fastsurfercnn.models.losses)": [[41, "FastSurferCNN.models.losses.DiceLoss", false]], "dicescore (class in cerebnet.utils.metrics)": [[30, "CerebNet.utils.metrics.DiceScore", false]], "dicescore (class in fastsurfercnn.utils.metrics)": [[56, "FastSurferCNN.utils.metrics.DiceScore", false]], "disable_confusion_mat() (fastsurfercnn.utils.meters.meter method)": [[55, "FastSurferCNN.utils.meters.Meter.disable_confusion_mat", false]], "download_checkpoint() (in module fastsurfercnn.utils.checkpoint)": [[49, "FastSurferCNN.utils.checkpoint.download_checkpoint", false]], "drop_disconnected_component() (in module cerebnet.datasets.wm_merge_clean)": [[21, "CerebNet.datasets.wm_merge_clean.drop_disconnected_component", false]], "empty() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.empty", false]], "enable_confusion_mat() (fastsurfercnn.utils.meters.meter method)": [[55, "FastSurferCNN.utils.meters.Meter.enable_confusion_mat", false]], "eval() (fastsurfercnn.inference.inference method)": [[39, "FastSurferCNN.inference.Inference.eval", false]], "eval() (hypvinn.inference.inference method)": [[64, "HypVINN.inference.Inference.eval", false]], "fastsurfercnn (class in cerebnet.models.networks)": [[23, "CerebNet.models.networks.FastSurferCNN", false]], "fastsurfercnn (class in fastsurfercnn.models.networks)": [[42, "FastSurferCNN.models.networks.FastSurferCNN", false]], "fastsurfercnn.data_loader.augmentation": [[32, "module-FastSurferCNN.data_loader.augmentation", false]], "fastsurfercnn.data_loader.conform": [[33, "module-FastSurferCNN.data_loader.conform", false]], "fastsurfercnn.data_loader.data_utils": [[34, "module-FastSurferCNN.data_loader.data_utils", false]], "fastsurfercnn.data_loader.dataset": [[35, "module-FastSurferCNN.data_loader.dataset", false]], "fastsurfercnn.data_loader.loader": [[36, "module-FastSurferCNN.data_loader.loader", false]], "fastsurfercnn.download_checkpoints": [[37, "module-FastSurferCNN.download_checkpoints", false]], "fastsurfercnn.generate_hdf5": [[38, "module-FastSurferCNN.generate_hdf5", false]], "fastsurfercnn.inference": [[39, "module-FastSurferCNN.inference", false]], "fastsurfercnn.models.interpolation_layer": [[40, "module-FastSurferCNN.models.interpolation_layer", false]], "fastsurfercnn.models.losses": [[41, "module-FastSurferCNN.models.losses", false]], "fastsurfercnn.models.networks": [[42, "module-FastSurferCNN.models.networks", false]], "fastsurfercnn.models.sub_module": [[43, "module-FastSurferCNN.models.sub_module", false]], "fastsurfercnn.quick_qc": [[44, "module-FastSurferCNN.quick_qc", false]], "fastsurfercnn.reduce_to_aseg": [[45, "module-FastSurferCNN.reduce_to_aseg", false]], "fastsurfercnn.run_prediction": [[46, "module-FastSurferCNN.run_prediction", false]], "fastsurfercnn.segstats": [[47, "module-FastSurferCNN.segstats", false]], "fastsurfercnn.utils.arg_types": [[48, "module-FastSurferCNN.utils.arg_types", false]], "fastsurfercnn.utils.checkpoint": [[49, "module-FastSurferCNN.utils.checkpoint", false]], "fastsurfercnn.utils.common": [[50, "module-FastSurferCNN.utils.common", false]], "fastsurfercnn.utils.load_config": [[51, "module-FastSurferCNN.utils.load_config", false]], "fastsurfercnn.utils.logging": [[52, "module-FastSurferCNN.utils.logging", false]], "fastsurfercnn.utils.lr_scheduler": [[53, "module-FastSurferCNN.utils.lr_scheduler", false]], "fastsurfercnn.utils.mapper": [[54, "module-FastSurferCNN.utils.mapper", false]], "fastsurfercnn.utils.meters": [[55, "module-FastSurferCNN.utils.meters", false]], "fastsurfercnn.utils.metrics": [[56, "module-FastSurferCNN.utils.metrics", false]], "fastsurfercnn.utils.misc": [[57, "module-FastSurferCNN.utils.misc", false]], "fastsurfercnn.utils.parser_defaults": [[58, "module-FastSurferCNN.utils.parser_defaults", false]], "fastsurfercnn.utils.run_tools": [[59, "module-FastSurferCNN.utils.run_tools", false]], "fastsurfercnn.utils.threads": [[60, "module-FastSurferCNN.utils.threads", false]], "fastsurfercnn.version": [[61, "module-FastSurferCNN.version", false]], "fastsurfercnnbase (class in fastsurfercnn.models.networks)": [[42, "FastSurferCNN.models.networks.FastSurferCNNBase", false]], "fastsurfervinn (class in fastsurfercnn.models.networks)": [[42, "FastSurferCNN.models.networks.FastSurferVINN", false]], "fileexists_by_attribute() (fastsurfercnn.utils.common.subjectdirectory method)": [[50, "FastSurferCNN.utils.common.SubjectDirectory.fileexists_by_attribute", false]], "fileexists_in_subject_folder() (fastsurfercnn.utils.common.subjectdirectory method)": [[50, "FastSurferCNN.utils.common.SubjectDirectory.fileexists_in_subject_folder", false]], "filename_by_attribute() (fastsurfercnn.utils.common.subjectdirectory method)": [[50, "FastSurferCNN.utils.common.SubjectDirectory.filename_by_attribute", false]], "filename_in_subject_folder() (fastsurfercnn.utils.common.subjectdirectory method)": [[50, "FastSurferCNN.utils.common.SubjectDirectory.filename_in_subject_folder", false]], "fill_unknown_labels_per_hemi() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.fill_unknown_labels_per_hemi", false]], "filling_unknown_labels() (in module cerebnet.datasets.wm_merge_clean)": [[21, "CerebNet.datasets.wm_merge_clean.filling_unknown_labels", false]], "filter_blank_slices_thick() (in module cerebnet.data_loader.data_utils)": [[15, "CerebNet.data_loader.data_utils.filter_blank_slices_thick", false]], "filter_blank_slices_thick() (in module cerebnet.datasets.utils)": [[20, "CerebNet.datasets.utils.filter_blank_slices_thick", false]], "filter_blank_slices_thick() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.filter_blank_slices_thick", false]], "filter_git_status() (in module fastsurfercnn.version)": [[61, "FastSurferCNN.version.filter_git_status", false]], "find_affine() (in module recon_surf.align_points)": [[68, "recon_surf.align_points.find_affine", false]], "find_all_islands() (in module recon_surf.sample_parc)": [[78, "recon_surf.sample_parc.find_all_islands", false]], "find_device() (in module fastsurfercnn.utils.common)": [[50, "FastSurferCNN.utils.common.find_device", false]], "find_img_size_by_fov() (in module fastsurfercnn.data_loader.conform)": [[33, "FastSurferCNN.data_loader.conform.find_img_size_by_fov", false]], "find_latest_experiment() (in module fastsurfercnn.utils.misc)": [[57, "FastSurferCNN.utils.misc.find_latest_experiment", false]], "find_min_size() (in module fastsurfercnn.data_loader.conform)": [[33, "FastSurferCNN.data_loader.conform.find_min_size", false]], "find_rigid() (in module recon_surf.align_points)": [[68, "recon_surf.align_points.find_rigid", false]], "find_rotation() (in module recon_surf.align_points)": [[68, "recon_surf.align_points.find_rotation", false]], "finish() (fastsurfercnn.utils.run_tools.popen method)": [[59, "FastSurferCNN.utils.run_tools.Popen.finish", false]], "flags (fastsurfercnn.utils.common.subjectlist property)": [[50, "FastSurferCNN.utils.common.SubjectList.flags", false]], "flip_wm_islands() (in module fastsurfercnn.reduce_to_aseg)": [[45, "FastSurferCNN.reduce_to_aseg.flip_wm_islands", false]], "float_gt_zero_and_le_one() (in module fastsurfercnn.utils.arg_types)": [[48, "FastSurferCNN.utils.arg_types.float_gt_zero_and_le_one", false]], "format_parameters() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.format_parameters", false]], "forward() (cerebnet.models.networks.fastsurfercnn method)": [[23, "CerebNet.models.networks.FastSurferCNN.forward", false]], "forward() (cerebnet.models.sub_module.classifierblock method)": [[24, "CerebNet.models.sub_module.ClassifierBlock.forward", false]], "forward() (cerebnet.models.sub_module.competitivedecoderblock method)": [[24, "CerebNet.models.sub_module.CompetitiveDecoderBlock.forward", false]], "forward() (cerebnet.models.sub_module.competitivedenseblock method)": [[24, "CerebNet.models.sub_module.CompetitiveDenseBlock.forward", false]], "forward() (cerebnet.models.sub_module.competitivedenseblockinput method)": [[24, "CerebNet.models.sub_module.CompetitiveDenseBlockInput.forward", false]], "forward() (cerebnet.models.sub_module.competitiveencoderblock method)": [[24, "CerebNet.models.sub_module.CompetitiveEncoderBlock.forward", false]], "forward() (cerebnet.models.sub_module.competitiveencoderblockinput method)": [[24, "CerebNet.models.sub_module.CompetitiveEncoderBlockInput.forward", false]], "forward() (fastsurfercnn.models.losses.combinedloss method)": [[41, "FastSurferCNN.models.losses.CombinedLoss.forward", false]], "forward() (fastsurfercnn.models.losses.crossentropy2d method)": [[41, "FastSurferCNN.models.losses.CrossEntropy2D.forward", false]], "forward() (fastsurfercnn.models.losses.diceloss method)": [[41, "FastSurferCNN.models.losses.DiceLoss.forward", false]], "forward() (fastsurfercnn.models.networks.fastsurfercnn method)": [[42, "FastSurferCNN.models.networks.FastSurferCNN.forward", false]], "forward() (fastsurfercnn.models.networks.fastsurfercnnbase method)": [[42, "FastSurferCNN.models.networks.FastSurferCNNBase.forward", false]], "forward() (fastsurfercnn.models.networks.fastsurfervinn method)": [[42, "FastSurferCNN.models.networks.FastSurferVINN.forward", false]], "forward() (fastsurfercnn.models.sub_module.classifierblock method)": [[43, "FastSurferCNN.models.sub_module.ClassifierBlock.forward", false]], "forward() (fastsurfercnn.models.sub_module.competitivedecoderblock method)": [[43, "FastSurferCNN.models.sub_module.CompetitiveDecoderBlock.forward", false]], "forward() (fastsurfercnn.models.sub_module.competitivedenseblock method)": [[43, "FastSurferCNN.models.sub_module.CompetitiveDenseBlock.forward", false]], "forward() (fastsurfercnn.models.sub_module.competitivedenseblockinput method)": [[43, "FastSurferCNN.models.sub_module.CompetitiveDenseBlockInput.forward", false]], "forward() (fastsurfercnn.models.sub_module.competitiveencoderblock method)": [[43, "FastSurferCNN.models.sub_module.CompetitiveEncoderBlock.forward", false]], "forward() (fastsurfercnn.models.sub_module.competitiveencoderblockinput method)": [[43, "FastSurferCNN.models.sub_module.CompetitiveEncoderBlockInput.forward", false]], "forward() (fastsurfercnn.models.sub_module.gaussiannoise method)": [[43, "FastSurferCNN.models.sub_module.GaussianNoise.forward", false]], "forward() (fastsurfercnn.models.sub_module.inputdenseblock method)": [[43, "FastSurferCNN.models.sub_module.InputDenseBlock.forward", false]], "forward() (fastsurfercnn.models.sub_module.outputdenseblock method)": [[43, "FastSurferCNN.models.sub_module.OutputDenseBlock.forward", false]], "forward() (hypvinn.models.networks.hypvinn method)": [[65, "HypVINN.models.networks.HypVINN.forward", false]], "fuse_cortex_labels() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.fuse_cortex_labels", false]], "gaussiannoise (class in fastsurfercnn.models.sub_module)": [[43, "FastSurferCNN.models.sub_module.GaussianNoise", false]], "get_adjm() (in module recon_surf.smooth_aparc)": [[79, "recon_surf.smooth_aparc.get_adjM", false]], "get_aseg_cereb_mask() (in module cerebnet.data_loader.data_utils)": [[15, "CerebNet.data_loader.data_utils.get_aseg_cereb_mask", false]], "get_attribute() (fastsurfercnn.utils.common.subjectdirectory method)": [[50, "FastSurferCNN.utils.common.SubjectDirectory.get_attribute", false]], "get_brain_centroid() (in module recon_surf.n4_bias_correct)": [[67, "recon_surf.N4_bias_correct.get_brain_centroid", false]], "get_cfg() (fastsurfercnn.inference.inference method)": [[39, "FastSurferCNN.inference.Inference.get_cfg", false]], "get_cfg() (hypvinn.inference.inference method)": [[64, "HypVINN.inference.Inference.get_cfg", false]], "get_checkpoint() (in module cerebnet.utils.checkpoint)": [[26, "CerebNet.utils.checkpoint.get_checkpoint", false]], "get_checkpoint() (in module fastsurfercnn.utils.checkpoint)": [[49, "FastSurferCNN.utils.checkpoint.get_checkpoint", false]], "get_checkpoint_path() (in module cerebnet.utils.checkpoint)": [[26, "CerebNet.utils.checkpoint.get_checkpoint_path", false]], "get_checkpoint_path() (in module fastsurfercnn.utils.checkpoint)": [[49, "FastSurferCNN.utils.checkpoint.get_checkpoint_path", false]], "get_checkpoints() (in module fastsurfercnn.utils.checkpoint)": [[49, "FastSurferCNN.utils.checkpoint.get_checkpoints", false]], "get_color_by_index() (fastsurfercnn.utils.mapper.colorlookuptable method)": [[54, "FastSurferCNN.utils.mapper.ColorLookupTable.get_color_by_index", false]], "get_common_suffix() (fastsurfercnn.utils.common.subjectlist method)": [[50, "FastSurferCNN.utils.common.SubjectList.get_common_suffix", false]], "get_config() (in module cerebnet.utils.load_config)": [[27, "CerebNet.utils.load_config.get_config", false]], "get_config() (in module fastsurfercnn.utils.load_config)": [[51, "FastSurferCNN.utils.load_config.get_config", false]], "get_conformed_vox_img_size() (in module fastsurfercnn.data_loader.conform)": [[33, "FastSurferCNN.data_loader.conform.get_conformed_vox_img_size", false]], "get_dataloader() (in module cerebnet.data_loader.loader)": [[17, "CerebNet.data_loader.loader.get_dataloader", false]], "get_dataloader() (in module fastsurfercnn.data_loader.loader)": [[36, "FastSurferCNN.data_loader.loader.get_dataloader", false]], "get_default_version_info() (in module fastsurfercnn.version)": [[61, "FastSurferCNN.version.get_default_version_info", false]], "get_device() (fastsurfercnn.inference.inference method)": [[39, "FastSurferCNN.inference.Inference.get_device", false]], "get_device() (hypvinn.inference.inference method)": [[64, "HypVINN.inference.Inference.get_device", false]], "get_epoch_lr() (cerebnet.utils.lr_scheduler.cosinelr method)": [[28, "CerebNet.utils.lr_scheduler.CosineLR.get_epoch_lr", false]], "get_image_mean() (in module recon_surf.n4_bias_correct)": [[67, "recon_surf.N4_bias_correct.get_image_mean", false]], "get_labels_from_lut() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.get_labels_from_lut", false]], "get_largest_cc() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.get_largest_cc", false]], "get_loss_func() (in module fastsurfercnn.models.losses)": [[41, "FastSurferCNN.models.losses.get_loss_func", false]], "get_lr() (cerebnet.utils.lr_scheduler.warmupcosinelr method)": [[28, "CerebNet.utils.lr_scheduler.WarmupCosineLR.get_lr", false]], "get_lr_scheduler() (in module cerebnet.utils.lr_scheduler)": [[28, "CerebNet.utils.lr_scheduler.get_lr_scheduler", false]], "get_lr_scheduler() (in module fastsurfercnn.utils.lr_scheduler)": [[53, "FastSurferCNN.utils.lr_scheduler.get_lr_scheduler", false]], "get_max_size() (fastsurfercnn.inference.inference method)": [[39, "FastSurferCNN.inference.Inference.get_max_size", false]], "get_max_size() (hypvinn.inference.inference method)": [[64, "HypVINN.inference.Inference.get_max_size", false]], "get_model_height() (fastsurfercnn.inference.inference method)": [[39, "FastSurferCNN.inference.Inference.get_model_height", false]], "get_model_height() (hypvinn.inference.inference method)": [[64, "HypVINN.inference.Inference.get_model_height", false]], "get_model_width() (fastsurfercnn.inference.inference method)": [[39, "FastSurferCNN.inference.Inference.get_model_width", false]], "get_model_width() (hypvinn.inference.inference method)": [[64, "HypVINN.inference.Inference.get_model_width", false]], "get_modelname() (fastsurfercnn.inference.inference method)": [[39, "FastSurferCNN.inference.Inference.get_modelname", false]], "get_modelname() (hypvinn.inference.inference method)": [[64, "HypVINN.inference.Inference.get_modelname", false]], "get_num_classes() (fastsurfercnn.inference.inference method)": [[39, "FastSurferCNN.inference.Inference.get_num_classes", false]], "get_num_classes() (fastsurfercnn.run_prediction.runmodelondata method)": [[46, "FastSurferCNN.run_prediction.RunModelOnData.get_num_classes", false]], "get_num_classes() (hypvinn.inference.inference method)": [[64, "HypVINN.inference.Inference.get_num_classes", false]], "get_num_threads() (in module fastsurfercnn.utils.threads)": [[60, "FastSurferCNN.utils.threads.get_num_threads", false]], "get_plane() (fastsurfercnn.inference.inference method)": [[39, "FastSurferCNN.inference.Inference.get_plane", false]], "get_plane() (hypvinn.inference.inference method)": [[64, "HypVINN.inference.Inference.get_plane", false]], "get_prediction() (fastsurfercnn.run_prediction.runmodelondata method)": [[46, "FastSurferCNN.run_prediction.RunModelOnData.get_prediction", false]], "get_prediction() (in module hypvinn.run_prediction)": [[66, "HypVINN.run_prediction.get_prediction", false]], "get_region_bg_intersection_mask() (in module fastsurfercnn.quick_qc)": [[44, "FastSurferCNN.quick_qc.get_region_bg_intersection_mask", false]], "get_seg_centroids() (in module recon_surf.align_seg)": [[69, "recon_surf.align_seg.get_seg_centroids", false]], "get_subject_names() (fastsurfercnn.data_loader.dataset.multiscaledataset method)": [[35, "FastSurferCNN.data_loader.dataset.MultiScaleDataset.get_subject_names", false]], "get_subject_names() (fastsurfercnn.data_loader.dataset.multiscaledatasetval method)": [[35, "FastSurferCNN.data_loader.dataset.MultiScaleDatasetVal.get_subject_names", false]], "get_tal_origin_voxel() (in module recon_surf.n4_bias_correct)": [[67, "recon_surf.N4_bias_correct.get_tal_origin_voxel", false]], "get_thick_slices() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.get_thick_slices", false]], "get_ventricle_bg_intersection_volume() (in module fastsurfercnn.quick_qc)": [[44, "FastSurferCNN.quick_qc.get_ventricle_bg_intersection_volume", false]], "get_vox2ras() (in module recon_surf.align_seg)": [[69, "recon_surf.align_seg.get_vox2ras", false]], "getitem_by_index() (fastsurfercnn.utils.mapper.colorlookuptable method)": [[54, "FastSurferCNN.utils.mapper.ColorLookupTable.getitem_by_index", false]], "getitem_by_index() (fastsurfercnn.utils.mapper.tsvlookuptable method)": [[54, "FastSurferCNN.utils.mapper.TSVLookupTable.getitem_by_index", false]], "getscale() (in module fastsurfercnn.data_loader.conform)": [[33, "FastSurferCNN.data_loader.conform.getscale", false]], "getsurfcorrespondence() (in module recon_surf.map_surf_label)": [[73, "recon_surf.map_surf_label.getSurfCorrespondence", false]], "global_stats() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.global_stats", false]], "h5pydataset (class in fastsurfercnn.generate_hdf5)": [[38, "FastSurferCNN.generate_hdf5.H5pyDataset", false]], "handle_cuda_memory_exception() (in module fastsurfercnn.utils.common)": [[50, "FastSurferCNN.utils.common.handle_cuda_memory_exception", false]], "has_attribute() (fastsurfercnn.utils.common.subjectdirectory method)": [[50, "FastSurferCNN.utils.common.SubjectDirectory.has_attribute", false]], "has_git() (in module fastsurfercnn.version)": [[61, "FastSurferCNN.version.has_git", false]], "hd() (in module cerebnet.utils.metrics)": [[30, "CerebNet.utils.metrics.hd", false]], "hd95() (in module cerebnet.utils.metrics)": [[30, "CerebNet.utils.metrics.hd95", false]], "helpformatter (class in fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.HelpFormatter", false]], "hypo_map_label2subseg() (in module hypvinn.data_loader.data_utils)": [[62, "HypVINN.data_loader.data_utils.hypo_map_label2subseg", false]], "hypo_map_prediction_sagittal2full() (in module hypvinn.data_loader.data_utils)": [[62, "HypVINN.data_loader.data_utils.hypo_map_prediction_sagittal2full", false]], "hypo_map_subseg_2_fsseg() (in module hypvinn.data_loader.data_utils)": [[62, "HypVINN.data_loader.data_utils.hypo_map_subseg_2_fsseg", false]], "hypvinn (class in hypvinn.models.networks)": [[65, "HypVINN.models.networks.HypVINN", false]], "hypvinn.data_loader.data_utils": [[62, "module-HypVINN.data_loader.data_utils", false]], "hypvinn.data_loader.dataset": [[63, "module-HypVINN.data_loader.dataset", false]], "hypvinn.inference": [[64, "module-HypVINN.inference", false]], "hypvinn.models.networks": [[65, "module-HypVINN.models.networks", false]], "hypvinn.run_prediction": [[66, "module-HypVINN.run_prediction", false]], "hypvinndataset (class in hypvinn.data_loader.dataset)": [[63, "HypVINN.data_loader.dataset.HypVINNDataset", false]], "id (fastsurfercnn.utils.common.subjectdirectory property)": [[50, "FastSurferCNN.utils.common.SubjectDirectory.id", false]], "infer_labels_excludeid() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.infer_labels_excludeid", false]], "infer_mapping_from_lut() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.infer_mapping_from_lut", false]], "infer_merged_labels() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.infer_merged_labels", false]], "inference (class in cerebnet.inference)": [[22, "CerebNet.inference.Inference", false]], "inference (class in fastsurfercnn.inference)": [[39, "FastSurferCNN.inference.Inference", false]], "inference (class in hypvinn.inference)": [[64, "HypVINN.inference.Inference", false]], "inputdenseblock (class in fastsurfercnn.models.sub_module)": [[43, "FastSurferCNN.models.sub_module.InputDenseBlock", false]], "int_ge_zero() (in module fastsurfercnn.utils.arg_types)": [[48, "FastSurferCNN.utils.arg_types.int_ge_zero", false]], "int_gt_zero() (in module fastsurfercnn.utils.arg_types)": [[48, "FastSurferCNN.utils.arg_types.int_gt_zero", false]], "iou_score() (in module fastsurfercnn.utils.metrics)": [[56, "FastSurferCNN.utils.metrics.iou_score", false]], "is_bijective() (fastsurfercnn.utils.mapper.mapper method)": [[54, "FastSurferCNN.utils.mapper.Mapper.is_bijective", false]], "is_checkpoint_epoch() (in module cerebnet.utils.checkpoint)": [[26, "CerebNet.utils.checkpoint.is_checkpoint_epoch", false]], "is_conform() (in module fastsurfercnn.data_loader.conform)": [[33, "FastSurferCNN.data_loader.conform.is_conform", false]], "is_int() (in module fastsurfercnn.utils.mapper)": [[54, "FastSurferCNN.utils.mapper.is_int", false]], "is_lia() (in module fastsurfercnn.data_loader.conform)": [[33, "FastSurferCNN.data_loader.conform.is_lia", false]], "is_resampling_vox2vox() (in module fastsurfercnn.data_loader.conform)": [[33, "FastSurferCNN.data_loader.conform.is_resampling_vox2vox", false]], "iterate() (in module fastsurfercnn.utils.common)": [[50, "FastSurferCNN.utils.common.iterate", false]], "itk_n4_bfcorrection() (in module recon_surf.n4_bias_correct)": [[67, "recon_surf.N4_bias_correct.itk_n4_bfcorrection", false]], "jsoncolorlookuptable (class in fastsurfercnn.utils.mapper)": [[54, "FastSurferCNN.utils.mapper.JsonColorLookupTable", false]], "labelname2id() (fastsurfercnn.utils.mapper.colorlookuptable method)": [[54, "FastSurferCNN.utils.mapper.ColorLookupTable.labelname2id", false]], "labelname2id() (fastsurfercnn.utils.mapper.jsoncolorlookuptable method)": [[54, "FastSurferCNN.utils.mapper.JsonColorLookupTable.labelname2id", false]], "labelname2id() (fastsurfercnn.utils.mapper.tsvlookuptable method)": [[54, "FastSurferCNN.utils.mapper.TSVLookupTable.labelname2id", false]], "labelname2index() (fastsurfercnn.utils.mapper.colorlookuptable method)": [[54, "FastSurferCNN.utils.mapper.ColorLookupTable.labelname2index", false]], "load_and_conform_image() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.load_and_conform_image", false]], "load_checkpoint() (fastsurfercnn.inference.inference method)": [[39, "FastSurferCNN.inference.Inference.load_checkpoint", false]], "load_checkpoint() (hypvinn.inference.inference method)": [[64, "HypVINN.inference.Inference.load_checkpoint", false]], "load_checkpoint_config() (in module fastsurfercnn.utils.checkpoint)": [[49, "FastSurferCNN.utils.checkpoint.load_checkpoint_config", false]], "load_checkpoint_config_defaults() (in module fastsurfercnn.utils.checkpoint)": [[49, "FastSurferCNN.utils.checkpoint.load_checkpoint_config_defaults", false]], "load_classwise_weights() (in module cerebnet.utils.misc)": [[31, "CerebNet.utils.misc.load_classwise_weights", false]], "load_config() (in module fastsurfercnn.utils.load_config)": [[51, "FastSurferCNN.utils.load_config.load_config", false]], "load_from_checkpoint() (in module cerebnet.utils.checkpoint)": [[26, "CerebNet.utils.checkpoint.load_from_checkpoint", false]], "load_from_checkpoint() (in module fastsurfercnn.utils.checkpoint)": [[49, "FastSurferCNN.utils.checkpoint.load_from_checkpoint", false]], "load_image() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.load_image", false]], "load_maybe_conform() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.load_maybe_conform", false]], "load_subject() (cerebnet.datasets.load_data.subjectloader method)": [[19, "CerebNet.datasets.load_data.SubjectLoader.load_subject", false]], "load_test_subject() (cerebnet.datasets.load_data.subjectloader method)": [[19, "CerebNet.datasets.load_data.SubjectLoader.load_test_subject", false]], "load_volumes() (in module hypvinn.run_prediction)": [[66, "HypVINN.run_prediction.load_volumes", false]], "locate_mask_bbox() (cerebnet.data_loader.dataset.subjectdataset method)": [[16, "CerebNet.data_loader.dataset.SubjectDataset.locate_mask_bbox", false]], "locating_unknowns() (in module cerebnet.datasets.wm_merge_clean)": [[21, "CerebNet.datasets.wm_merge_clean.locating_unknowns", false]], "log_epoch() (cerebnet.utils.meters.meter method)": [[29, "CerebNet.utils.meters.Meter.log_epoch", false]], "log_epoch() (fastsurfercnn.utils.meters.meter method)": [[55, "FastSurferCNN.utils.meters.Meter.log_epoch", false]], "log_iter() (cerebnet.utils.meters.meter method)": [[29, "CerebNet.utils.meters.Meter.log_iter", false]], "log_iter() (fastsurfercnn.utils.meters.meter method)": [[55, "FastSurferCNN.utils.meters.Meter.log_iter", false]], "log_lr() (cerebnet.utils.meters.meter method)": [[29, "CerebNet.utils.meters.Meter.log_lr", false]], "lr_func_cosine() (cerebnet.utils.lr_scheduler.cosinelr method)": [[28, "CerebNet.utils.lr_scheduler.CosineLR.lr_func_cosine", false]], "ltadict (class in cerebnet.datasets.utils)": [[20, "CerebNet.datasets.utils.LTADict", false]], "main() (in module cerebnet.apply_warp)": [[13, "CerebNet.apply_warp.main", false]], "main() (in module cerebnet.run_prediction)": [[25, "CerebNet.run_prediction.main", false]], "main() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.main", false]], "main() (in module fastsurfercnn.version)": [[61, "FastSurferCNN.version.main", false]], "main() (in module hypvinn.run_prediction)": [[66, "HypVINN.run_prediction.main", false]], "main() (in module recon_surf.smooth_aparc)": [[79, "recon_surf.smooth_aparc.main", false]], "main_segfile (fastsurfercnn.utils.common.subjectdirectory property)": [[50, "FastSurferCNN.utils.common.SubjectDirectory.main_segfile", false]], "make_arguments() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.make_arguments", false]], "make_classmapper() (fastsurfercnn.utils.mapper.mapper class method)": [[54, "FastSurferCNN.utils.mapper.Mapper.make_classmapper", false]], "make_parser() (in module fastsurfercnn.data_loader.conform)": [[33, "FastSurferCNN.data_loader.conform.make_parser", false]], "make_parser() (in module fastsurfercnn.run_prediction)": [[46, "FastSurferCNN.run_prediction.make_parser", false]], "make_parser() (in module fastsurfercnn.version)": [[61, "FastSurferCNN.version.make_parser", false]], "make_parser() (in module recon_surf.rewrite_oriented_surface)": [[76, "recon_surf.rewrite_oriented_surface.make_parser", false]], "make_subjects_dir() (fastsurfercnn.utils.common.subjectlist method)": [[50, "FastSurferCNN.utils.common.SubjectList.make_subjects_dir", false]], "map() (fastsurfercnn.utils.common.serialexecutor method)": [[50, "FastSurferCNN.utils.common.SerialExecutor.map", false]], "map() (fastsurfercnn.utils.mapper.mapper method)": [[54, "FastSurferCNN.utils.mapper.Mapper.map", false]], "map_aparc_aseg2label() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.map_aparc_aseg2label", false]], "map_image() (in module fastsurfercnn.data_loader.conform)": [[33, "FastSurferCNN.data_loader.conform.map_image", false]], "map_label2aparc_aseg() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.map_label2aparc_aseg", false]], "map_label2subseg() (in module cerebnet.datasets.utils)": [[20, "CerebNet.datasets.utils.map_label2subseg", false]], "map_multiple_labels() (in module recon_surf.create_annotation)": [[70, "recon_surf.create_annotation.map_multiple_labels", false]], "map_prediction_sagittal2full() (in module cerebnet.data_loader.data_utils)": [[15, "CerebNet.data_loader.data_utils.map_prediction_sagittal2full", false]], "map_prediction_sagittal2full() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.map_prediction_sagittal2full", false]], "map_sag2label() (in module cerebnet.data_loader.data_utils)": [[15, "CerebNet.data_loader.data_utils.map_sag2label", false]], "map_size() (in module cerebnet.datasets.utils)": [[20, "CerebNet.datasets.utils.map_size", false]], "mapper (class in fastsurfercnn.utils.mapper)": [[54, "FastSurferCNN.utils.mapper.Mapper", false]], "mapsurflabel() (in module recon_surf.map_surf_label)": [[73, "recon_surf.map_surf_label.mapSurfLabel", false]], "max_label (fastsurfercnn.utils.mapper.mapper property)": [[54, "FastSurferCNN.utils.mapper.Mapper.max_label", false]], "messagebuffer (class in fastsurfercnn.utils.run_tools)": [[59, "FastSurferCNN.utils.run_tools.MessageBuffer", false]], "meter (class in cerebnet.utils.meters)": [[29, "CerebNet.utils.meters.Meter", false]], "meter (class in fastsurfercnn.utils.meters)": [[55, "FastSurferCNN.utils.meters.Meter", false]], "metrics_per_class() (cerebnet.utils.meters.testmeter method)": [[29, "CerebNet.utils.meters.TestMeter.metrics_per_class", false]], "mode_filter() (in module recon_surf.smooth_aparc)": [[79, "recon_surf.smooth_aparc.mode_filter", false]], "module": [[13, "module-CerebNet.apply_warp", false], [14, "module-CerebNet.data_loader.augmentation", false], [15, "module-CerebNet.data_loader.data_utils", false], [16, "module-CerebNet.data_loader.dataset", false], [17, "module-CerebNet.data_loader.loader", false], [18, "module-CerebNet.datasets.generate_hdf5", false], [19, "module-CerebNet.datasets.load_data", false], [20, "module-CerebNet.datasets.utils", false], [21, "module-CerebNet.datasets.wm_merge_clean", false], [22, "module-CerebNet.inference", false], [23, "module-CerebNet.models.networks", false], [24, "module-CerebNet.models.sub_module", false], [25, "module-CerebNet.run_prediction", false], [26, "module-CerebNet.utils.checkpoint", false], [27, "module-CerebNet.utils.load_config", false], [28, "module-CerebNet.utils.lr_scheduler", false], [29, "module-CerebNet.utils.meters", false], [30, "module-CerebNet.utils.metrics", false], [31, "module-CerebNet.utils.misc", false], [32, "module-FastSurferCNN.data_loader.augmentation", false], [33, "module-FastSurferCNN.data_loader.conform", false], [34, "module-FastSurferCNN.data_loader.data_utils", false], [35, "module-FastSurferCNN.data_loader.dataset", false], [36, "module-FastSurferCNN.data_loader.loader", false], [37, "module-FastSurferCNN.download_checkpoints", false], [38, "module-FastSurferCNN.generate_hdf5", false], [39, "module-FastSurferCNN.inference", false], [40, "module-FastSurferCNN.models.interpolation_layer", false], [41, "module-FastSurferCNN.models.losses", false], [42, "module-FastSurferCNN.models.networks", false], [43, "module-FastSurferCNN.models.sub_module", false], [44, "module-FastSurferCNN.quick_qc", false], [45, "module-FastSurferCNN.reduce_to_aseg", false], [46, "module-FastSurferCNN.run_prediction", false], [47, "module-FastSurferCNN.segstats", false], [48, "module-FastSurferCNN.utils.arg_types", false], [49, "module-FastSurferCNN.utils.checkpoint", false], [50, "module-FastSurferCNN.utils.common", false], [51, "module-FastSurferCNN.utils.load_config", false], [52, "module-FastSurferCNN.utils.logging", false], [53, "module-FastSurferCNN.utils.lr_scheduler", false], [54, "module-FastSurferCNN.utils.mapper", false], [55, "module-FastSurferCNN.utils.meters", false], [56, "module-FastSurferCNN.utils.metrics", false], [57, "module-FastSurferCNN.utils.misc", false], [58, "module-FastSurferCNN.utils.parser_defaults", false], [59, "module-FastSurferCNN.utils.run_tools", false], [60, "module-FastSurferCNN.utils.threads", false], [61, "module-FastSurferCNN.version", false], [62, "module-HypVINN.data_loader.data_utils", false], [63, "module-HypVINN.data_loader.dataset", false], [64, "module-HypVINN.inference", false], [65, "module-HypVINN.models.networks", false], [66, "module-HypVINN.run_prediction", false], [67, "module-recon_surf.N4_bias_correct", false], [68, "module-recon_surf.align_points", false], [69, "module-recon_surf.align_seg", false], [70, "module-recon_surf.create_annotation", false], [71, "module-recon_surf.fs_balabels", false], [72, "module-recon_surf.lta", false], [73, "module-recon_surf.map_surf_label", false], [74, "module-recon_surf.paint_cc_into_pred", false], [75, "module-recon_surf.rewrite_mc_surface", false], [76, "module-recon_surf.rewrite_oriented_surface", false], [77, "module-recon_surf.rotate_sphere", false], [78, "module-recon_surf.sample_parc", false], [79, "module-recon_surf.smooth_aparc", false], [80, "module-recon_surf.spherically_project_wrapper", false]], "multiscaledataset (class in fastsurfercnn.data_loader.dataset)": [[35, "FastSurferCNN.data_loader.dataset.MultiScaleDataset", false]], "multiscaledatasetval (class in fastsurfercnn.data_loader.dataset)": [[35, "FastSurferCNN.data_loader.dataset.MultiScaleDatasetVal", false]], "multiscaleorigdatathickslices (class in fastsurfercnn.data_loader.dataset)": [[35, "FastSurferCNN.data_loader.dataset.MultiScaleOrigDataThickSlices", false]], "name (fastsurfercnn.utils.mapper.colorlookuptable property)": [[54, "FastSurferCNN.utils.mapper.ColorLookupTable.name", false]], "name (fastsurfercnn.utils.mapper.mapper property)": [[54, "FastSurferCNN.utils.mapper.Mapper.name", false]], "normalize_img() (in module recon_surf.n4_bias_correct)": [[67, "recon_surf.N4_bias_correct.normalize_img", false]], "normalize_wm_aseg() (in module recon_surf.n4_bias_correct)": [[67, "recon_surf.N4_bias_correct.normalize_wm_aseg", false]], "normalize_wm_mask_ball() (in module recon_surf.n4_bias_correct)": [[67, "recon_surf.N4_bias_correct.normalize_wm_mask_ball", false]], "option_parse() (in module hypvinn.run_prediction)": [[66, "HypVINN.run_prediction.option_parse", false]], "optional_path() (in module hypvinn.run_prediction)": [[66, "HypVINN.run_prediction.optional_path", false]], "options_parse() (in module fastsurfercnn.data_loader.conform)": [[33, "FastSurferCNN.data_loader.conform.options_parse", false]], "options_parse() (in module fastsurfercnn.quick_qc)": [[44, "FastSurferCNN.quick_qc.options_parse", false]], "options_parse() (in module fastsurfercnn.reduce_to_aseg)": [[45, "FastSurferCNN.reduce_to_aseg.options_parse", false]], "options_parse() (in module recon_surf.align_seg)": [[69, "recon_surf.align_seg.options_parse", false]], "options_parse() (in module recon_surf.create_annotation)": [[70, "recon_surf.create_annotation.options_parse", false]], "options_parse() (in module recon_surf.fs_balabels)": [[71, "recon_surf.fs_balabels.options_parse", false]], "options_parse() (in module recon_surf.map_surf_label)": [[73, "recon_surf.map_surf_label.options_parse", false]], "options_parse() (in module recon_surf.n4_bias_correct)": [[67, "recon_surf.N4_bias_correct.options_parse", false]], "options_parse() (in module recon_surf.rewrite_mc_surface)": [[75, "recon_surf.rewrite_mc_surface.options_parse", false]], "options_parse() (in module recon_surf.rotate_sphere)": [[77, "recon_surf.rotate_sphere.options_parse", false]], "options_parse() (in module recon_surf.sample_parc)": [[78, "recon_surf.sample_parc.options_parse", false]], "options_parse() (in module recon_surf.smooth_aparc)": [[79, "recon_surf.smooth_aparc.options_parse", false]], "orig_name (fastsurfercnn.utils.common.subjectdirectory property)": [[50, "FastSurferCNN.utils.common.SubjectDirectory.orig_name", false]], "outputdenseblock (class in fastsurfercnn.models.sub_module)": [[43, "FastSurferCNN.models.sub_module.OutputDenseBlock", false]], "pad_slicer() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.pad_slicer", false]], "paint_in_cc() (in module recon_surf.paint_cc_into_pred)": [[74, "recon_surf.paint_cc_into_pred.paint_in_cc", false]], "parse_build_file() (in module fastsurfercnn.version)": [[61, "FastSurferCNN.version.parse_build_file", false]], "parse_files() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.parse_files", false]], "parse_version() (in module recon_surf.fs_balabels)": [[71, "recon_surf.fs_balabels.parse_version", false]], "patch_filter() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.patch_filter", false]], "patch_neighbors() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.patch_neighbors", false]], "pipeline() (in module fastsurfercnn.utils.common)": [[50, "FastSurferCNN.utils.common.pipeline", false]], "pipeline_conform_and_save_orig() (fastsurfercnn.run_prediction.runmodelondata method)": [[46, "FastSurferCNN.run_prediction.RunModelOnData.pipeline_conform_and_save_orig", false]], "plane (cerebnet.data_loader.dataset.subjectdataset property)": [[16, "CerebNet.data_loader.dataset.SubjectDataset.plane", false]], "plot_confusion_matrix() (in module cerebnet.utils.misc)": [[31, "CerebNet.utils.misc.plot_confusion_matrix", false]], "plot_confusion_matrix() (in module fastsurfercnn.utils.misc)": [[57, "FastSurferCNN.utils.misc.plot_confusion_matrix", false]], "plot_predictions() (in module cerebnet.utils.misc)": [[31, "CerebNet.utils.misc.plot_predictions", false]], "plot_predictions() (in module fastsurfercnn.utils.misc)": [[57, "FastSurferCNN.utils.misc.plot_predictions", false]], "pool (fastsurfercnn.run_prediction.runmodelondata property)": [[46, "FastSurferCNN.run_prediction.RunModelOnData.pool", false]], "popen (class in fastsurfercnn.utils.run_tools)": [[59, "FastSurferCNN.utils.run_tools.Popen", false]], "precision_recall() (in module fastsurfercnn.utils.metrics)": [[56, "FastSurferCNN.utils.metrics.precision_recall", false]], "prediction_visualize() (cerebnet.utils.meters.meter method)": [[29, "CerebNet.utils.meters.Meter.prediction_visualize", false]], "prepare_checkpoints() (in module hypvinn.run_prediction)": [[66, "HypVINN.run_prediction.prepare_checkpoints", false]], "preproc_image() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.preproc_image", false]], "print_build_file() (in module fastsurfercnn.version)": [[61, "FastSurferCNN.version.print_build_file", false]], "pv_calc() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.pv_calc", false]], "pv_calc_patch() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.pv_calc_patch", false]], "pvstats (class in fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.PVStats", false]], "pypopen (class in fastsurfercnn.utils.run_tools)": [[59, "FastSurferCNN.utils.run_tools.PyPopen", false]], "randomaffine (class in cerebnet.data_loader.augmentation)": [[14, "CerebNet.data_loader.augmentation.RandomAffine", false]], "randombiasfield (class in cerebnet.data_loader.augmentation)": [[14, "CerebNet.data_loader.augmentation.RandomBiasField", false]], "randomflip (class in cerebnet.data_loader.augmentation)": [[14, "CerebNet.data_loader.augmentation.RandomFlip", false]], "randomlabelstoimage (class in cerebnet.data_loader.augmentation)": [[14, "CerebNet.data_loader.augmentation.RandomLabelsToImage", false]], "read_and_close_version() (in module fastsurfercnn.version)": [[61, "FastSurferCNN.version.read_and_close_version", false]], "read_classes_from_lut() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.read_classes_from_lut", false]], "read_colortable() (in module recon_surf.create_annotation)": [[70, "recon_surf.create_annotation.read_colortable", false]], "read_colortables() (in module recon_surf.fs_balabels)": [[71, "recon_surf.fs_balabels.read_colortables", false]], "read_lta() (in module cerebnet.datasets.utils)": [[20, "CerebNet.datasets.utils.read_lta", false]], "read_multiple_labels() (in module recon_surf.create_annotation)": [[70, "recon_surf.create_annotation.read_multiple_labels", false]], "read_talairach_xfm() (in module recon_surf.n4_bias_correct)": [[67, "recon_surf.N4_bias_correct.read_talairach_xfm", false]], "read_version_from_project_file() (in module fastsurfercnn.version)": [[61, "FastSurferCNN.version.read_version_from_project_file", false]], "recon_surf.align_points": [[68, "module-recon_surf.align_points", false]], "recon_surf.align_seg": [[69, "module-recon_surf.align_seg", false]], "recon_surf.create_annotation": [[70, "module-recon_surf.create_annotation", false]], "recon_surf.fs_balabels": [[71, "module-recon_surf.fs_balabels", false]], "recon_surf.lta": [[72, "module-recon_surf.lta", false]], "recon_surf.map_surf_label": [[73, "module-recon_surf.map_surf_label", false]], "recon_surf.n4_bias_correct": [[67, "module-recon_surf.N4_bias_correct", false]], "recon_surf.paint_cc_into_pred": [[74, "module-recon_surf.paint_cc_into_pred", false]], "recon_surf.rewrite_mc_surface": [[75, "module-recon_surf.rewrite_mc_surface", false]], "recon_surf.rewrite_oriented_surface": [[76, "module-recon_surf.rewrite_oriented_surface", false]], "recon_surf.rotate_sphere": [[77, "module-recon_surf.rotate_sphere", false]], "recon_surf.sample_parc": [[78, "module-recon_surf.sample_parc", false]], "recon_surf.smooth_aparc": [[79, "module-recon_surf.smooth_aparc", false]], "recon_surf.spherically_project_wrapper": [[80, "module-recon_surf.spherically_project_wrapper", false]], "reduce_to_aseg() (in module fastsurfercnn.reduce_to_aseg)": [[45, "FastSurferCNN.reduce_to_aseg.reduce_to_aseg", false]], "reducelronplateauwithrestarts (class in cerebnet.utils.lr_scheduler)": [[28, "CerebNet.utils.lr_scheduler.ReduceLROnPlateauWithRestarts", false]], "remove_ckpt() (in module fastsurfercnn.utils.checkpoint)": [[49, "FastSurferCNN.utils.checkpoint.remove_ckpt", false]], "reorient_img() (in module hypvinn.data_loader.data_utils)": [[62, "HypVINN.data_loader.data_utils.reorient_img", false]], "replace_labels() (in module recon_surf.sample_parc)": [[78, "recon_surf.sample_parc.replace_labels", false]], "resafe_surface() (in module recon_surf.rewrite_mc_surface)": [[75, "recon_surf.rewrite_mc_surface.resafe_surface", false]], "resafe_surface() (in module recon_surf.rewrite_oriented_surface)": [[76, "recon_surf.rewrite_oriented_surface.resafe_surface", false]], "rescale() (in module fastsurfercnn.data_loader.conform)": [[33, "FastSurferCNN.data_loader.conform.rescale", false]], "rescale_image() (in module hypvinn.data_loader.data_utils)": [[62, "HypVINN.data_loader.data_utils.rescale_image", false]], "reset() (cerebnet.utils.meters.meter method)": [[29, "CerebNet.utils.meters.Meter.reset", false]], "reset() (cerebnet.utils.metrics.dicescore method)": [[30, "CerebNet.utils.metrics.DiceScore.reset", false]], "reset() (fastsurfercnn.utils.meters.meter method)": [[55, "FastSurferCNN.utils.meters.Meter.reset", false]], "reset() (fastsurfercnn.utils.metrics.dicescore method)": [[56, "FastSurferCNN.utils.metrics.DiceScore.reset", false]], "reversed_dict() (fastsurfercnn.utils.mapper.mapper method)": [[54, "FastSurferCNN.utils.mapper.Mapper.reversed_dict", false]], "rmat2angles() (in module recon_surf.align_points)": [[68, "recon_surf.align_points.rmat2angles", false]], "roi (cerebnet.data_loader.dataset.subjectdataset attribute)": [[16, "CerebNet.data_loader.dataset.SubjectDataset.roi", false]], "run() (fastsurfercnn.inference.inference method)": [[39, "FastSurferCNN.inference.Inference.run", false]], "run() (hypvinn.inference.inference method)": [[64, "HypVINN.inference.Inference.run", false]], "runmodelondata (class in fastsurfercnn.run_prediction)": [[46, "FastSurferCNN.run_prediction.RunModelOnData", false]], "sagittal_coronal_remap_lookup() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.sagittal_coronal_remap_lookup", false]], "sample_img() (in module recon_surf.sample_parc)": [[78, "recon_surf.sample_parc.sample_img", false]], "sample_intensity_stats_from_image() (in module cerebnet.data_loader.augmentation)": [[14, "CerebNet.data_loader.augmentation.sample_intensity_stats_from_image", false]], "sample_nearest_nonzero() (in module recon_surf.sample_parc)": [[78, "recon_surf.sample_parc.sample_nearest_nonzero", false]], "sample_parc() (in module recon_surf.sample_parc)": [[78, "recon_surf.sample_parc.sample_parc", false]], "save_checkpoint() (in module cerebnet.utils.checkpoint)": [[26, "CerebNet.utils.checkpoint.save_checkpoint", false]], "save_checkpoint() (in module fastsurfercnn.utils.checkpoint)": [[49, "FastSurferCNN.utils.checkpoint.save_checkpoint", false]], "save_image() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.save_image", false]], "save_img() (fastsurfercnn.run_prediction.runmodelondata method)": [[46, "FastSurferCNN.run_prediction.RunModelOnData.save_img", false]], "save_mgh_image() (in module cerebnet.datasets.wm_merge_clean)": [[21, "CerebNet.datasets.wm_merge_clean.save_mgh_image", false]], "save_nii_image() (in module cerebnet.apply_warp)": [[13, "CerebNet.apply_warp.save_nii_image", false]], "scalecrop() (in module fastsurfercnn.data_loader.conform)": [[33, "FastSurferCNN.data_loader.conform.scalecrop", false]], "section() (in module fastsurfercnn.version)": [[61, "FastSurferCNN.version.section", false]], "seg_borders() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.seg_borders", false]], "segfile (fastsurfercnn.utils.common.subjectdirectory property)": [[50, "FastSurferCNN.utils.common.SubjectDirectory.segfile", false]], "serialexecutor (class in fastsurfercnn.utils.common)": [[50, "FastSurferCNN.utils.common.SerialExecutor", false]], "set_cfg() (fastsurfercnn.inference.inference method)": [[39, "FastSurferCNN.inference.Inference.set_cfg", false]], "set_cfg() (hypvinn.inference.inference method)": [[64, "HypVINN.inference.Inference.set_cfg", false]], "set_lr() (cerebnet.utils.lr_scheduler.cosinelr method)": [[28, "CerebNet.utils.lr_scheduler.CosineLR.set_lr", false]], "set_model() (fastsurfercnn.run_prediction.runmodelondata method)": [[46, "FastSurferCNN.run_prediction.RunModelOnData.set_model", false]], "set_model() (hypvinn.inference.inference method)": [[64, "HypVINN.inference.Inference.set_model", false]], "set_plane() (cerebnet.data_loader.dataset.subjectdataset method)": [[16, "CerebNet.data_loader.dataset.SubjectDataset.set_plane", false]], "set_summary_path() (in module cerebnet.utils.misc)": [[31, "CerebNet.utils.misc.set_summary_path", false]], "set_up_cfgs() (in module fastsurfercnn.run_prediction)": [[46, "FastSurferCNN.run_prediction.set_up_cfgs", false]], "set_up_cfgs() (in module hypvinn.run_prediction)": [[66, "HypVINN.run_prediction.set_up_cfgs", false]], "set_up_model_params() (fastsurfercnn.run_prediction.runmodelondata method)": [[46, "FastSurferCNN.run_prediction.RunModelOnData.set_up_model_params", false]], "setup_logging() (in module fastsurfercnn.utils.logging)": [[52, "FastSurferCNN.utils.logging.setup_logging", false]], "setup_model() (fastsurfercnn.inference.inference method)": [[39, "FastSurferCNN.inference.Inference.setup_model", false]], "setup_model() (hypvinn.inference.inference method)": [[64, "HypVINN.inference.Inference.setup_model", false]], "setup_options() (in module cerebnet.run_prediction)": [[25, "CerebNet.run_prediction.setup_options", false]], "setup_options() (in module recon_surf.spherically_project_wrapper)": [[80, "recon_surf.spherically_project_wrapper.setup_options", false]], "slice_lia2ras() (in module cerebnet.data_loader.data_utils)": [[15, "CerebNet.data_loader.data_utils.slice_lia2ras", false]], "slice_ras2lia() (in module cerebnet.data_loader.data_utils)": [[15, "CerebNet.data_loader.data_utils.slice_ras2lia", false]], "smooth_aparc() (in module recon_surf.smooth_aparc)": [[79, "recon_surf.smooth_aparc.smooth_aparc", false]], "source_space (fastsurfercnn.utils.mapper.mapper property)": [[54, "FastSurferCNN.utils.mapper.Mapper.source_space", false]], "sphere() (in module cerebnet.datasets.wm_merge_clean)": [[21, "CerebNet.datasets.wm_merge_clean.sphere", false]], "spherical_wrapper() (in module recon_surf.spherically_project_wrapper)": [[80, "recon_surf.spherically_project_wrapper.spherical_wrapper", false]], "split_cortex_labels() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.split_cortex_labels", false]], "step() (cerebnet.utils.lr_scheduler.reducelronplateauwithrestarts method)": [[28, "CerebNet.utils.lr_scheduler.ReduceLROnPlateauWithRestarts.step", false]], "subject_dir (fastsurfercnn.utils.common.subjectdirectory property)": [[50, "FastSurferCNN.utils.common.SubjectDirectory.subject_dir", false]], "subjectdataset (class in cerebnet.data_loader.dataset)": [[16, "CerebNet.data_loader.dataset.SubjectDataset", false]], "subjectdirectory (class in fastsurfercnn.utils.common)": [[50, "FastSurferCNN.utils.common.SubjectDirectory", false]], "subjectdirectoryconfig (class in fastsurfercnn.utils.parser_defaults)": [[58, "FastSurferCNN.utils.parser_defaults.SubjectDirectoryConfig", false]], "subjectlist (class in fastsurfercnn.utils.common)": [[50, "FastSurferCNN.utils.common.SubjectList", false]], "subjectloader (class in cerebnet.datasets.load_data)": [[19, "CerebNet.datasets.load_data.SubjectLoader", false]], "submit() (fastsurfercnn.utils.common.serialexecutor method)": [[50, "FastSurferCNN.utils.common.SerialExecutor.submit", false]], "table_to_dataframe() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.table_to_dataframe", false]], "target_dtype() (in module fastsurfercnn.utils.arg_types)": [[48, "FastSurferCNN.utils.arg_types.target_dtype", false]], "target_space (fastsurfercnn.utils.mapper.mapper property)": [[54, "FastSurferCNN.utils.mapper.Mapper.target_space", false]], "testloader (class in cerebnet.data_loader.dataset)": [[16, "CerebNet.data_loader.dataset.TestLoader", false]], "testmeter (class in cerebnet.utils.meters)": [[29, "CerebNet.utils.meters.TestMeter", false]], "to() (fastsurfercnn.inference.inference method)": [[39, "FastSurferCNN.inference.Inference.to", false]], "to_same_type() (in module fastsurfercnn.utils.mapper)": [[54, "FastSurferCNN.utils.mapper.to_same_type", false]], "totensor (class in cerebnet.data_loader.augmentation)": [[14, "CerebNet.data_loader.augmentation.ToTensor", false]], "totensor (class in fastsurfercnn.data_loader.augmentation)": [[32, "FastSurferCNN.data_loader.augmentation.ToTensor", false]], "totensortest (class in cerebnet.data_loader.augmentation)": [[14, "CerebNet.data_loader.augmentation.ToTensorTest", false]], "totensortest (class in fastsurfercnn.data_loader.augmentation)": [[32, "FastSurferCNN.data_loader.augmentation.ToTensorTest", false]], "transform() (fastsurfercnn.generate_hdf5.h5pydataset method)": [[38, "FastSurferCNN.generate_hdf5.H5pyDataset.transform", false]], "transform_axial() (in module cerebnet.data_loader.data_utils)": [[15, "CerebNet.data_loader.data_utils.transform_axial", false]], "transform_axial() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.transform_axial", false]], "transform_axial2coronal() (in module hypvinn.data_loader.data_utils)": [[62, "HypVINN.data_loader.data_utils.transform_axial2coronal", false]], "transform_axial2sagittal() (in module cerebnet.data_loader.data_utils)": [[15, "CerebNet.data_loader.data_utils.transform_axial2sagittal", false]], "transform_axial2sagittal() (in module hypvinn.data_loader.data_utils)": [[62, "HypVINN.data_loader.data_utils.transform_axial2sagittal", false]], "transform_coronal() (in module cerebnet.data_loader.data_utils)": [[15, "CerebNet.data_loader.data_utils.transform_coronal", false]], "transform_sagittal() (in module cerebnet.data_loader.data_utils)": [[15, "CerebNet.data_loader.data_utils.transform_sagittal", false]], "transform_sagittal() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.transform_sagittal", false]], "tsvlookuptable (class in fastsurfercnn.utils.mapper)": [[54, "FastSurferCNN.utils.mapper.TSVLookupTable", false]], "uniform_filter() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.uniform_filter", false]], "unify_imgs() (fastsurfercnn.data_loader.dataset.multiscaledataset method)": [[35, "FastSurferCNN.data_loader.dataset.MultiScaleDataset.unify_imgs", false]], "unify_lateralized_labels() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.unify_lateralized_labels", false]], "unquote_str() (in module fastsurfercnn.utils.arg_types)": [[48, "FastSurferCNN.utils.arg_types.unquote_str", false]], "update() (cerebnet.utils.metrics.dicescore method)": [[30, "CerebNet.utils.metrics.DiceScore.update", false]], "update() (fastsurfercnn.utils.mapper.mapper method)": [[54, "FastSurferCNN.utils.mapper.Mapper.update", false]], "update() (fastsurfercnn.utils.metrics.dicescore method)": [[56, "FastSurferCNN.utils.metrics.DiceScore.update", false]], "update_num_steps() (in module fastsurfercnn.utils.misc)": [[57, "FastSurferCNN.utils.misc.update_num_steps", false]], "update_results_dir() (in module cerebnet.utils.misc)": [[31, "CerebNet.utils.misc.update_results_dir", false]], "update_split_path() (in module cerebnet.utils.misc)": [[31, "CerebNet.utils.misc.update_split_path", false]], "update_stats() (cerebnet.utils.meters.meter method)": [[29, "CerebNet.utils.meters.Meter.update_stats", false]], "update_stats() (fastsurfercnn.utils.meters.meter method)": [[55, "FastSurferCNN.utils.meters.Meter.update_stats", false]], "update_structnames() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.update_structnames", false]], "versiondict (class in fastsurfercnn.version)": [[61, "FastSurferCNN.version.VersionDict", false]], "visualize_batch() (in module cerebnet.utils.misc)": [[31, "CerebNet.utils.misc.visualize_batch", false]], "volume_similarity() (in module cerebnet.utils.metrics)": [[30, "CerebNet.utils.metrics.volume_similarity", false]], "vox_size() (in module fastsurfercnn.utils.arg_types)": [[48, "FastSurferCNN.utils.arg_types.vox_size", false]], "warmupcosinelr (class in cerebnet.utils.lr_scheduler)": [[28, "CerebNet.utils.lr_scheduler.WarmupCosineLR", false]], "write_annot() (in module recon_surf.create_annotation)": [[70, "recon_surf.create_annotation.write_annot", false]], "write_statsfile() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.write_statsfile", false]], "write_summary() (cerebnet.utils.meters.meter method)": [[29, "CerebNet.utils.meters.Meter.write_summary", false]], "write_summary() (fastsurfercnn.utils.meters.meter method)": [[55, "FastSurferCNN.utils.meters.Meter.write_summary", false]], "writelta() (in module recon_surf.lta)": [[72, "recon_surf.lta.writeLTA", false]], "writesurflabel() (in module recon_surf.map_surf_label)": [[73, "recon_surf.map_surf_label.writeSurfLabel", false]], "zeropad2d (class in fastsurfercnn.data_loader.augmentation)": [[32, "FastSurferCNN.data_loader.augmentation.ZeroPad2D", false]], "zeropad2dtest (class in fastsurfercnn.data_loader.augmentation)": [[32, "FastSurferCNN.data_loader.augmentation.ZeroPad2DTest", false]], "zoom2d (class in fastsurfercnn.models.interpolation_layer)": [[40, "FastSurferCNN.models.interpolation_layer.Zoom2d", false]], "zoom3d (class in fastsurfercnn.models.interpolation_layer)": [[40, "FastSurferCNN.models.interpolation_layer.Zoom3d", false]]}, "objects": {"CerebNet": [[13, 0, 0, "-", "apply_warp"], [22, 0, 0, "-", "inference"], [25, 0, 0, "-", "run_prediction"]], "CerebNet.apply_warp": [[13, 1, 1, "", "main"], [13, 1, 1, "", "save_nii_image"]], "CerebNet.data_loader": [[14, 0, 0, "-", "augmentation"], [15, 0, 0, "-", "data_utils"], [16, 0, 0, "-", "dataset"], [17, 0, 0, "-", "loader"]], "CerebNet.data_loader.augmentation": [[14, 2, 1, "", "RandomAffine"], [14, 2, 1, "", "RandomBiasField"], [14, 2, 1, "", "RandomFlip"], [14, 2, 1, "", "RandomLabelsToImage"], [14, 2, 1, "", "ToTensor"], [14, 2, 1, "", "ToTensorTest"], [14, 1, 1, "", "sample_intensity_stats_from_image"]], "CerebNet.data_loader.data_utils": [[15, 1, 1, "", "create_weight_mask2d"], [15, 1, 1, "", "filter_blank_slices_thick"], [15, 1, 1, "", "get_aseg_cereb_mask"], [15, 1, 1, "", "map_prediction_sagittal2full"], [15, 1, 1, "", "map_sag2label"], [15, 1, 1, "", "slice_lia2ras"], [15, 1, 1, "", "slice_ras2lia"], [15, 1, 1, "", "transform_axial"], [15, 1, 1, "", "transform_axial2sagittal"], [15, 1, 1, "", "transform_coronal"], [15, 1, 1, "", "transform_sagittal"]], "CerebNet.data_loader.dataset": [[16, 2, 1, "", "CerebDataset"], [16, 2, 1, "", "SubjectDataset"], [16, 2, 1, "", "TestLoader"]], "CerebNet.data_loader.dataset.SubjectDataset": [[16, 3, 1, "", "locate_mask_bbox"], [16, 4, 1, "", "plane"], [16, 5, 1, "", "roi"], [16, 3, 1, "", "set_plane"]], "CerebNet.data_loader.loader": [[17, 1, 1, "", "get_dataloader"]], "CerebNet.datasets": [[18, 0, 0, "-", "generate_hdf5"], [19, 0, 0, "-", "load_data"], [20, 0, 0, "-", "utils"], [21, 0, 0, "-", "wm_merge_clean"]], "CerebNet.datasets.generate_hdf5": [[18, 2, 1, "", "CerebNetDataset"]], "CerebNet.datasets.generate_hdf5.CerebNetDataset": [[18, 3, 1, "", "create_hdf5_dataset"]], "CerebNet.datasets.load_data": [[19, 2, 1, "", "SubjectLoader"]], "CerebNet.datasets.load_data.SubjectLoader": [[19, 3, 1, "", "load_subject"], [19, 3, 1, "", "load_test_subject"]], "CerebNet.datasets.utils": [[20, 2, 1, "", "LTADict"], [20, 1, 1, "", "bounding_volume_offset"], [20, 1, 1, "", "crop_transform"], [20, 1, 1, "", "filter_blank_slices_thick"], [20, 1, 1, "", "map_label2subseg"], [20, 1, 1, "", "map_size"], [20, 1, 1, "", "read_lta"]], "CerebNet.datasets.wm_merge_clean": [[21, 1, 1, "", "add_cereb_wm"], [21, 1, 1, "", "cereb_subseg_lateral_mask"], [21, 1, 1, "", "correct_cereb_brainstem"], [21, 1, 1, "", "drop_disconnected_component"], [21, 1, 1, "", "filling_unknown_labels"], [21, 1, 1, "", "locating_unknowns"], [21, 1, 1, "", "save_mgh_image"], [21, 1, 1, "", "sphere"]], "CerebNet.inference": [[22, 2, 1, "", "Inference"]], "CerebNet.models": [[23, 0, 0, "-", "networks"], [24, 0, 0, "-", "sub_module"]], "CerebNet.models.networks": [[23, 2, 1, "", "FastSurferCNN"], [23, 1, 1, "", "build_model"]], "CerebNet.models.networks.FastSurferCNN": [[23, 3, 1, "", "forward"]], "CerebNet.models.sub_module": [[24, 2, 1, "", "ClassifierBlock"], [24, 2, 1, "", "CompetitiveDecoderBlock"], [24, 2, 1, "", "CompetitiveDenseBlock"], [24, 2, 1, "", "CompetitiveDenseBlockInput"], [24, 2, 1, "", "CompetitiveEncoderBlock"], [24, 2, 1, "", "CompetitiveEncoderBlockInput"]], "CerebNet.models.sub_module.ClassifierBlock": [[24, 3, 1, "", "forward"]], "CerebNet.models.sub_module.CompetitiveDecoderBlock": [[24, 3, 1, "", "forward"]], "CerebNet.models.sub_module.CompetitiveDenseBlock": [[24, 3, 1, "", "forward"]], "CerebNet.models.sub_module.CompetitiveDenseBlockInput": [[24, 3, 1, "", "forward"]], "CerebNet.models.sub_module.CompetitiveEncoderBlock": [[24, 3, 1, "", "forward"]], "CerebNet.models.sub_module.CompetitiveEncoderBlockInput": [[24, 3, 1, "", "forward"]], "CerebNet.run_prediction": [[25, 1, 1, "", "main"], [25, 1, 1, "", "setup_options"]], "CerebNet.utils": [[26, 0, 0, "-", "checkpoint"], [27, 0, 0, "-", "load_config"], [28, 0, 0, "-", "lr_scheduler"], [29, 0, 0, "-", "meters"], [30, 0, 0, "-", "metrics"], [31, 0, 0, "-", "misc"]], "CerebNet.utils.checkpoint": [[26, 1, 1, "", "create_checkpoint_dir"], [26, 1, 1, "", "get_checkpoint"], [26, 1, 1, "", "get_checkpoint_path"], [26, 1, 1, "", "is_checkpoint_epoch"], [26, 1, 1, "", "load_from_checkpoint"], [26, 1, 1, "", "save_checkpoint"]], "CerebNet.utils.load_config": [[27, 1, 1, "", "get_config"]], "CerebNet.utils.lr_scheduler": [[28, 2, 1, "", "CosineAnnealingWarmRestartsDecay"], [28, 2, 1, "", "CosineLR"], [28, 2, 1, "", "ReduceLROnPlateauWithRestarts"], [28, 2, 1, "", "WarmupCosineLR"], [28, 1, 1, "", "get_lr_scheduler"]], "CerebNet.utils.lr_scheduler.CosineAnnealingWarmRestartsDecay": [[28, 3, 1, "", "decay_base_lr"]], "CerebNet.utils.lr_scheduler.CosineLR": [[28, 3, 1, "", "get_epoch_lr"], [28, 3, 1, "", "lr_func_cosine"], [28, 3, 1, "", "set_lr"]], "CerebNet.utils.lr_scheduler.ReduceLROnPlateauWithRestarts": [[28, 3, 1, "", "step"]], "CerebNet.utils.lr_scheduler.WarmupCosineLR": [[28, 3, 1, "", "get_lr"]], "CerebNet.utils.meters": [[29, 2, 1, "", "Meter"], [29, 2, 1, "", "TestMeter"]], "CerebNet.utils.meters.Meter": [[29, 3, 1, "", "log_epoch"], [29, 3, 1, "", "log_iter"], [29, 3, 1, "", "log_lr"], [29, 3, 1, "", "prediction_visualize"], [29, 3, 1, "", "reset"], [29, 3, 1, "", "update_stats"], [29, 3, 1, "", "write_summary"]], "CerebNet.utils.meters.TestMeter": [[29, 3, 1, "", "metrics_per_class"]], "CerebNet.utils.metrics": [[30, 2, 1, "", "DiceScore"], [30, 1, 1, "", "dice_score"], [30, 1, 1, "", "hd"], [30, 1, 1, "", "hd95"], [30, 1, 1, "", "volume_similarity"]], "CerebNet.utils.metrics.DiceScore": [[30, 3, 1, "", "compute"], [30, 3, 1, "", "reset"], [30, 3, 1, "", "update"]], "CerebNet.utils.misc": [[31, 1, 1, "", "load_classwise_weights"], [31, 1, 1, "", "plot_confusion_matrix"], [31, 1, 1, "", "plot_predictions"], [31, 1, 1, "", "set_summary_path"], [31, 1, 1, "", "update_results_dir"], [31, 1, 1, "", "update_split_path"], [31, 1, 1, "", "visualize_batch"]], "FastSurferCNN": [[37, 0, 0, "-", "download_checkpoints"], [38, 0, 0, "-", "generate_hdf5"], [39, 0, 0, "-", "inference"], [44, 0, 0, "-", "quick_qc"], [45, 0, 0, "-", "reduce_to_aseg"], [46, 0, 0, "-", "run_prediction"], [47, 0, 0, "-", "segstats"], [61, 0, 0, "-", "version"]], "FastSurferCNN.data_loader": [[32, 0, 0, "-", "augmentation"], [33, 0, 0, "-", "conform"], [34, 0, 0, "-", "data_utils"], [35, 0, 0, "-", "dataset"], [36, 0, 0, "-", "loader"]], "FastSurferCNN.data_loader.augmentation": [[32, 2, 1, "", "AddGaussianNoise"], [32, 2, 1, "", "AugmentationPadImage"], [32, 2, 1, "", "AugmentationRandomCrop"], [32, 2, 1, "", "ToTensor"], [32, 2, 1, "", "ToTensorTest"], [32, 2, 1, "", "ZeroPad2D"], [32, 2, 1, "", "ZeroPad2DTest"]], "FastSurferCNN.data_loader.conform": [[33, 2, 1, "", "Criteria"], [33, 1, 1, "", "check_affine_in_nifti"], [33, 1, 1, "", "conform"], [33, 1, 1, "", "find_img_size_by_fov"], [33, 1, 1, "", "find_min_size"], [33, 1, 1, "", "get_conformed_vox_img_size"], [33, 1, 1, "", "getscale"], [33, 1, 1, "", "is_conform"], [33, 1, 1, "", "is_lia"], [33, 1, 1, "", "is_resampling_vox2vox"], [33, 1, 1, "", "make_parser"], [33, 1, 1, "", "map_image"], [33, 1, 1, "", "options_parse"], [33, 1, 1, "", "rescale"], [33, 1, 1, "", "scalecrop"]], "FastSurferCNN.data_loader.data_utils": [[34, 1, 1, "", "bbox_3d"], [34, 1, 1, "", "clean_cortex_labels"], [34, 1, 1, "", "cortex_border_mask"], [34, 1, 1, "", "create_weight_mask"], [34, 1, 1, "", "deep_sulci_and_wm_strand_mask"], [34, 1, 1, "", "fill_unknown_labels_per_hemi"], [34, 1, 1, "", "filter_blank_slices_thick"], [34, 1, 1, "", "fuse_cortex_labels"], [34, 1, 1, "", "get_labels_from_lut"], [34, 1, 1, "", "get_largest_cc"], [34, 1, 1, "", "get_thick_slices"], [34, 1, 1, "", "infer_mapping_from_lut"], [34, 1, 1, "", "load_and_conform_image"], [34, 1, 1, "", "load_image"], [34, 1, 1, "", "load_maybe_conform"], [34, 1, 1, "", "map_aparc_aseg2label"], [34, 1, 1, "", "map_label2aparc_aseg"], [34, 1, 1, "", "map_prediction_sagittal2full"], [34, 1, 1, "", "read_classes_from_lut"], [34, 1, 1, "", "sagittal_coronal_remap_lookup"], [34, 1, 1, "", "save_image"], [34, 1, 1, "", "split_cortex_labels"], [34, 1, 1, "", "transform_axial"], [34, 1, 1, "", "transform_sagittal"], [34, 1, 1, "", "unify_lateralized_labels"]], "FastSurferCNN.data_loader.dataset": [[35, 2, 1, "", "MultiScaleDataset"], [35, 2, 1, "", "MultiScaleDatasetVal"], [35, 2, 1, "", "MultiScaleOrigDataThickSlices"]], "FastSurferCNN.data_loader.dataset.MultiScaleDataset": [[35, 3, 1, "", "get_subject_names"], [35, 3, 1, "", "unify_imgs"]], "FastSurferCNN.data_loader.dataset.MultiScaleDatasetVal": [[35, 3, 1, "", "get_subject_names"]], "FastSurferCNN.data_loader.loader": [[36, 1, 1, "", "get_dataloader"]], "FastSurferCNN.generate_hdf5": [[38, 2, 1, "", "H5pyDataset"]], "FastSurferCNN.generate_hdf5.H5pyDataset": [[38, 3, 1, "", "create_hdf5_dataset"], [38, 3, 1, "", "transform"]], "FastSurferCNN.inference": [[39, 2, 1, "", "Inference"]], "FastSurferCNN.inference.Inference": [[39, 3, 1, "", "eval"], [39, 3, 1, "", "get_cfg"], [39, 3, 1, "", "get_device"], [39, 3, 1, "", "get_max_size"], [39, 3, 1, "", "get_model_height"], [39, 3, 1, "", "get_model_width"], [39, 3, 1, "", "get_modelname"], [39, 3, 1, "", "get_num_classes"], [39, 3, 1, "", "get_plane"], [39, 3, 1, "", "load_checkpoint"], [39, 3, 1, "", "run"], [39, 3, 1, "", "set_cfg"], [39, 3, 1, "", "setup_model"], [39, 3, 1, "", "to"]], "FastSurferCNN.models": [[40, 0, 0, "-", "interpolation_layer"], [41, 0, 0, "-", "losses"], [42, 0, 0, "-", "networks"], [43, 0, 0, "-", "sub_module"]], "FastSurferCNN.models.interpolation_layer": [[40, 2, 1, "", "Zoom2d"], [40, 2, 1, "", "Zoom3d"]], "FastSurferCNN.models.interpolation_layer.Zoom2d": [[40, 4, 1, "", "crop_position"]], "FastSurferCNN.models.interpolation_layer.Zoom3d": [[40, 4, 1, "", "crop_position"]], "FastSurferCNN.models.losses": [[41, 2, 1, "", "CombinedLoss"], [41, 2, 1, "", "CrossEntropy2D"], [41, 2, 1, "", "DiceLoss"], [41, 1, 1, "", "get_loss_func"]], "FastSurferCNN.models.losses.CombinedLoss": [[41, 3, 1, "", "forward"]], "FastSurferCNN.models.losses.CrossEntropy2D": [[41, 3, 1, "", "forward"]], "FastSurferCNN.models.losses.DiceLoss": [[41, 3, 1, "", "forward"]], "FastSurferCNN.models.networks": [[42, 2, 1, "", "FastSurferCNN"], [42, 2, 1, "", "FastSurferCNNBase"], [42, 2, 1, "", "FastSurferVINN"], [42, 1, 1, "", "build_model"]], "FastSurferCNN.models.networks.FastSurferCNN": [[42, 3, 1, "", "forward"]], "FastSurferCNN.models.networks.FastSurferCNNBase": [[42, 3, 1, "", "forward"]], "FastSurferCNN.models.networks.FastSurferVINN": [[42, 3, 1, "", "forward"]], "FastSurferCNN.models.sub_module": [[43, 2, 1, "", "ClassifierBlock"], [43, 2, 1, "", "CompetitiveDecoderBlock"], [43, 2, 1, "", "CompetitiveDenseBlock"], [43, 2, 1, "", "CompetitiveDenseBlockInput"], [43, 2, 1, "", "CompetitiveEncoderBlock"], [43, 2, 1, "", "CompetitiveEncoderBlockInput"], [43, 2, 1, "", "GaussianNoise"], [43, 2, 1, "", "InputDenseBlock"], [43, 2, 1, "", "OutputDenseBlock"]], "FastSurferCNN.models.sub_module.ClassifierBlock": [[43, 3, 1, "", "forward"]], "FastSurferCNN.models.sub_module.CompetitiveDecoderBlock": [[43, 3, 1, "", "forward"]], "FastSurferCNN.models.sub_module.CompetitiveDenseBlock": [[43, 3, 1, "", "forward"]], "FastSurferCNN.models.sub_module.CompetitiveDenseBlockInput": [[43, 3, 1, "", "forward"]], "FastSurferCNN.models.sub_module.CompetitiveEncoderBlock": [[43, 3, 1, "", "forward"]], "FastSurferCNN.models.sub_module.CompetitiveEncoderBlockInput": [[43, 3, 1, "", "forward"]], "FastSurferCNN.models.sub_module.GaussianNoise": [[43, 3, 1, "", "forward"]], "FastSurferCNN.models.sub_module.InputDenseBlock": [[43, 3, 1, "", "forward"]], "FastSurferCNN.models.sub_module.OutputDenseBlock": [[43, 3, 1, "", "forward"]], "FastSurferCNN.quick_qc": [[44, 1, 1, "", "check_volume"], [44, 1, 1, "", "get_region_bg_intersection_mask"], [44, 1, 1, "", "get_ventricle_bg_intersection_volume"], [44, 1, 1, "", "options_parse"]], "FastSurferCNN.reduce_to_aseg": [[45, 1, 1, "", "create_mask"], [45, 1, 1, "", "flip_wm_islands"], [45, 1, 1, "", "options_parse"], [45, 1, 1, "", "reduce_to_aseg"]], "FastSurferCNN.run_prediction": [[46, 2, 1, "", "RunModelOnData"], [46, 1, 1, "", "args2cfg"], [46, 1, 1, "", "make_parser"], [46, 1, 1, "", "set_up_cfgs"]], "FastSurferCNN.run_prediction.RunModelOnData": [[46, 3, 1, "", "async_save_img"], [46, 3, 1, "", "conform_and_save_orig"], [46, 3, 1, "", "get_num_classes"], [46, 3, 1, "", "get_prediction"], [46, 3, 1, "", "pipeline_conform_and_save_orig"], [46, 4, 1, "", "pool"], [46, 3, 1, "", "save_img"], [46, 3, 1, "", "set_model"], [46, 3, 1, "", "set_up_model_params"]], "FastSurferCNN.segstats": [[47, 2, 1, "", "HelpFormatter"], [47, 2, 1, "", "PVStats"], [47, 1, 1, "", "add_measure_parser"], [47, 1, 1, "", "add_two_help_messages"], [47, 1, 1, "", "borders"], [47, 1, 1, "", "calculate_merged_labels"], [47, 1, 1, "", "check_shape_affine"], [47, 1, 1, "", "crop_patch_to_mask"], [47, 1, 1, "", "empty"], [47, 1, 1, "", "format_parameters"], [47, 1, 1, "", "global_stats"], [47, 1, 1, "", "infer_labels_excludeid"], [47, 1, 1, "", "infer_merged_labels"], [47, 1, 1, "", "main"], [47, 1, 1, "", "make_arguments"], [47, 1, 1, "", "pad_slicer"], [47, 1, 1, "", "parse_files"], [47, 1, 1, "", "patch_filter"], [47, 1, 1, "", "patch_neighbors"], [47, 1, 1, "", "preproc_image"], [47, 1, 1, "", "pv_calc"], [47, 1, 1, "", "pv_calc_patch"], [47, 1, 1, "", "seg_borders"], [47, 1, 1, "", "table_to_dataframe"], [47, 1, 1, "", "uniform_filter"], [47, 1, 1, "", "update_structnames"], [47, 1, 1, "", "write_statsfile"]], "FastSurferCNN.utils": [[48, 0, 0, "-", "arg_types"], [49, 0, 0, "-", "checkpoint"], [50, 0, 0, "-", "common"], [51, 0, 0, "-", "load_config"], [52, 0, 0, "-", "logging"], [53, 0, 0, "-", "lr_scheduler"], [54, 0, 0, "-", "mapper"], [55, 0, 0, "-", "meters"], [56, 0, 0, "-", "metrics"], [57, 0, 0, "-", "misc"], [58, 0, 0, "-", "parser_defaults"], [59, 0, 0, "-", "run_tools"], [60, 0, 0, "-", "threads"]], "FastSurferCNN.utils.arg_types": [[48, 1, 1, "", "float_gt_zero_and_le_one"], [48, 1, 1, "", "int_ge_zero"], [48, 1, 1, "", "int_gt_zero"], [48, 1, 1, "", "target_dtype"], [48, 1, 1, "", "unquote_str"], [48, 1, 1, "", "vox_size"]], "FastSurferCNN.utils.checkpoint": [[49, 2, 1, "", "CheckpointConfigDict"], [49, 1, 1, "", "check_and_download_ckpts"], [49, 1, 1, "", "create_checkpoint_dir"], [49, 1, 1, "", "download_checkpoint"], [49, 1, 1, "", "get_checkpoint"], [49, 1, 1, "", "get_checkpoint_path"], [49, 1, 1, "", "get_checkpoints"], [49, 1, 1, "", "load_checkpoint_config"], [49, 1, 1, "", "load_checkpoint_config_defaults"], [49, 1, 1, "", "load_from_checkpoint"], [49, 1, 1, "", "remove_ckpt"], [49, 1, 1, "", "save_checkpoint"]], "FastSurferCNN.utils.common": [[50, 2, 1, "", "SerialExecutor"], [50, 2, 1, "", "SubjectDirectory"], [50, 2, 1, "", "SubjectList"], [50, 1, 1, "", "assert_no_root"], [50, 1, 1, "", "find_device"], [50, 1, 1, "", "handle_cuda_memory_exception"], [50, 1, 1, "", "iterate"], [50, 1, 1, "", "pipeline"]], "FastSurferCNN.utils.common.SerialExecutor": [[50, 3, 1, "", "map"], [50, 3, 1, "", "submit"]], "FastSurferCNN.utils.common.SubjectDirectory": [[50, 4, 1, "", "asegdkt_segfile"], [50, 3, 1, "", "can_resolve_attribute"], [50, 3, 1, "", "can_resolve_filename"], [50, 4, 1, "", "conf_name"], [50, 4, 1, "", "copy_orig_name"], [50, 3, 1, "", "fileexists_by_attribute"], [50, 3, 1, "", "fileexists_in_subject_folder"], [50, 3, 1, "", "filename_by_attribute"], [50, 3, 1, "", "filename_in_subject_folder"], [50, 3, 1, "", "get_attribute"], [50, 3, 1, "", "has_attribute"], [50, 4, 1, "", "id"], [50, 4, 1, "", "main_segfile"], [50, 4, 1, "", "orig_name"], [50, 4, 1, "", "segfile"], [50, 4, 1, "", "subject_dir"]], "FastSurferCNN.utils.common.SubjectList": [[50, 3, 1, "", "are_all_subject_files"], [50, 4, 1, "", "flags"], [50, 3, 1, "", "get_common_suffix"], [50, 3, 1, "", "make_subjects_dir"]], "FastSurferCNN.utils.load_config": [[51, 1, 1, "", "get_config"], [51, 1, 1, "", "load_config"]], "FastSurferCNN.utils.logging": [[52, 1, 1, "", "setup_logging"]], "FastSurferCNN.utils.lr_scheduler": [[53, 1, 1, "", "get_lr_scheduler"]], "FastSurferCNN.utils.mapper": [[54, 2, 1, "", "ColorLookupTable"], [54, 2, 1, "", "JsonColorLookupTable"], [54, 2, 1, "", "Mapper"], [54, 2, 1, "", "TSVLookupTable"], [54, 1, 1, "", "is_int"], [54, 1, 1, "", "to_same_type"]], "FastSurferCNN.utils.mapper.ColorLookupTable": [[54, 4, 1, "", "classes"], [54, 4, 1, "", "color_palette"], [54, 3, 1, "", "colormap"], [54, 3, 1, "", "get_color_by_index"], [54, 3, 1, "", "getitem_by_index"], [54, 3, 1, "", "labelname2id"], [54, 3, 1, "", "labelname2index"], [54, 4, 1, "", "name"]], "FastSurferCNN.utils.mapper.JsonColorLookupTable": [[54, 3, 1, "", "dataframe"], [54, 3, 1, "", "labelname2id"]], "FastSurferCNN.utils.mapper.Mapper": [[54, 3, 1, "", "chain"], [54, 3, 1, "", "is_bijective"], [54, 3, 1, "", "make_classmapper"], [54, 3, 1, "", "map"], [54, 4, 1, "", "max_label"], [54, 4, 1, "", "name"], [54, 3, 1, "", "reversed_dict"], [54, 4, 1, "", "source_space"], [54, 4, 1, "", "target_space"], [54, 3, 1, "", "update"]], "FastSurferCNN.utils.mapper.TSVLookupTable": [[54, 3, 1, "", "dataframe"], [54, 3, 1, "", "getitem_by_index"], [54, 3, 1, "", "labelname2id"]], "FastSurferCNN.utils.meters": [[55, 2, 1, "", "Meter"]], "FastSurferCNN.utils.meters.Meter": [[55, 3, 1, "", "disable_confusion_mat"], [55, 3, 1, "", "enable_confusion_mat"], [55, 3, 1, "", "log_epoch"], [55, 3, 1, "", "log_iter"], [55, 3, 1, "", "reset"], [55, 3, 1, "", "update_stats"], [55, 3, 1, "", "write_summary"]], "FastSurferCNN.utils.metrics": [[56, 2, 1, "", "DiceScore"], [56, 1, 1, "", "dice_score"], [56, 1, 1, "", "iou_score"], [56, 1, 1, "", "precision_recall"]], "FastSurferCNN.utils.metrics.DiceScore": [[56, 3, 1, "", "comput_dice_cnf"], [56, 3, 1, "", "compute_dsc"], [56, 3, 1, "", "reset"], [56, 3, 1, "", "update"]], "FastSurferCNN.utils.misc": [[57, 1, 1, "", "check_path"], [57, 1, 1, "", "find_latest_experiment"], [57, 1, 1, "", "plot_confusion_matrix"], [57, 1, 1, "", "plot_predictions"], [57, 1, 1, "", "update_num_steps"]], "FastSurferCNN.utils.parser_defaults": [[58, 2, 1, "", "CanAddArguments"], [58, 2, 1, "", "SubjectDirectoryConfig"], [58, 1, 1, "", "add_arguments"], [58, 1, 1, "", "add_plane_flags"]], "FastSurferCNN.utils.parser_defaults.CanAddArguments": [[58, 3, 1, "", "add_argument"]], "FastSurferCNN.utils.run_tools": [[59, 2, 1, "", "MessageBuffer"], [59, 2, 1, "", "Popen"], [59, 2, 1, "", "PyPopen"]], "FastSurferCNN.utils.run_tools.Popen": [[59, 3, 1, "", "as_future"], [59, 3, 1, "", "finish"]], "FastSurferCNN.utils.threads": [[60, 1, 1, "", "get_num_threads"]], "FastSurferCNN.version": [[61, 2, 1, "", "VersionDict"], [61, 1, 1, "", "filter_git_status"], [61, 1, 1, "", "get_default_version_info"], [61, 1, 1, "", "has_git"], [61, 1, 1, "", "main"], [61, 1, 1, "", "make_parser"], [61, 1, 1, "", "parse_build_file"], [61, 1, 1, "", "print_build_file"], [61, 1, 1, "", "read_and_close_version"], [61, 1, 1, "", "read_version_from_project_file"], [61, 1, 1, "", "section"]], "HypVINN": [[64, 0, 0, "-", "inference"], [66, 0, 0, "-", "run_prediction"]], "HypVINN.data_loader": [[62, 0, 0, "-", "data_utils"], [63, 0, 0, "-", "dataset"]], "HypVINN.data_loader.data_utils": [[62, 1, 1, "", "calculate_flip_orientation"], [62, 1, 1, "", "hypo_map_label2subseg"], [62, 1, 1, "", "hypo_map_prediction_sagittal2full"], [62, 1, 1, "", "hypo_map_subseg_2_fsseg"], [62, 1, 1, "", "reorient_img"], [62, 1, 1, "", "rescale_image"], [62, 1, 1, "", "transform_axial2coronal"], [62, 1, 1, "", "transform_axial2sagittal"]], "HypVINN.data_loader.dataset": [[63, 2, 1, "", "HypVINNDataset"]], "HypVINN.inference": [[64, 2, 1, "", "Inference"]], "HypVINN.inference.Inference": [[64, 3, 1, "", "eval"], [64, 3, 1, "", "get_cfg"], [64, 3, 1, "", "get_device"], [64, 3, 1, "", "get_max_size"], [64, 3, 1, "", "get_model_height"], [64, 3, 1, "", "get_model_width"], [64, 3, 1, "", "get_modelname"], [64, 3, 1, "", "get_num_classes"], [64, 3, 1, "", "get_plane"], [64, 3, 1, "", "load_checkpoint"], [64, 3, 1, "", "run"], [64, 3, 1, "", "set_cfg"], [64, 3, 1, "", "set_model"], [64, 3, 1, "", "setup_model"]], "HypVINN.models": [[65, 0, 0, "-", "networks"]], "HypVINN.models.networks": [[65, 2, 1, "", "HypVINN"], [65, 1, 1, "", "build_model"]], "HypVINN.models.networks.HypVINN": [[65, 3, 1, "", "forward"]], "HypVINN.run_prediction": [[66, 1, 1, "", "get_prediction"], [66, 1, 1, "", "load_volumes"], [66, 1, 1, "", "main"], [66, 1, 1, "", "option_parse"], [66, 1, 1, "", "optional_path"], [66, 1, 1, "", "prepare_checkpoints"], [66, 1, 1, "", "set_up_cfgs"]], "recon_surf": [[67, 0, 0, "-", "N4_bias_correct"], [68, 0, 0, "-", "align_points"], [69, 0, 0, "-", "align_seg"], [70, 0, 0, "-", "create_annotation"], [71, 0, 0, "-", "fs_balabels"], [72, 0, 0, "-", "lta"], [73, 0, 0, "-", "map_surf_label"], [74, 0, 0, "-", "paint_cc_into_pred"], [75, 0, 0, "-", "rewrite_mc_surface"], [76, 0, 0, "-", "rewrite_oriented_surface"], [77, 0, 0, "-", "rotate_sphere"], [78, 0, 0, "-", "sample_parc"], [79, 0, 0, "-", "smooth_aparc"], [80, 0, 0, "-", "spherically_project_wrapper"]], "recon_surf.N4_bias_correct": [[67, 1, 1, "", "get_brain_centroid"], [67, 1, 1, "", "get_image_mean"], [67, 1, 1, "", "get_tal_origin_voxel"], [67, 1, 1, "", "itk_n4_bfcorrection"], [67, 1, 1, "", "normalize_img"], [67, 1, 1, "", "normalize_wm_aseg"], [67, 1, 1, "", "normalize_wm_mask_ball"], [67, 1, 1, "", "options_parse"], [67, 1, 1, "", "read_talairach_xfm"]], "recon_surf.align_points": [[68, 1, 1, "", "angles2rmat"], [68, 1, 1, "", "find_affine"], [68, 1, 1, "", "find_rigid"], [68, 1, 1, "", "find_rotation"], [68, 1, 1, "", "rmat2angles"]], "recon_surf.align_seg": [[69, 1, 1, "", "align_flipped"], [69, 1, 1, "", "align_seg_centroids"], [69, 1, 1, "", "get_seg_centroids"], [69, 1, 1, "", "get_vox2ras"], [69, 1, 1, "", "options_parse"]], "recon_surf.create_annotation": [[70, 1, 1, "", "build_annot"], [70, 1, 1, "", "create_annotation"], [70, 1, 1, "", "map_multiple_labels"], [70, 1, 1, "", "options_parse"], [70, 1, 1, "", "read_colortable"], [70, 1, 1, "", "read_multiple_labels"], [70, 1, 1, "", "write_annot"]], "recon_surf.fs_balabels": [[71, 1, 1, "", "options_parse"], [71, 1, 1, "", "parse_version"], [71, 1, 1, "", "read_colortables"]], "recon_surf.lta": [[72, 1, 1, "", "writeLTA"]], "recon_surf.map_surf_label": [[73, 1, 1, "", "getSurfCorrespondence"], [73, 1, 1, "", "mapSurfLabel"], [73, 1, 1, "", "options_parse"], [73, 1, 1, "", "writeSurfLabel"]], "recon_surf.paint_cc_into_pred": [[74, 1, 1, "", "argument_parse"], [74, 1, 1, "", "paint_in_cc"]], "recon_surf.rewrite_mc_surface": [[75, 1, 1, "", "options_parse"], [75, 1, 1, "", "resafe_surface"]], "recon_surf.rewrite_oriented_surface": [[76, 1, 1, "", "make_parser"], [76, 1, 1, "", "resafe_surface"]], "recon_surf.rotate_sphere": [[77, 1, 1, "", "align_aparc_centroids"], [77, 1, 1, "", "options_parse"]], "recon_surf.sample_parc": [[78, 1, 1, "", "construct_adj_cluster"], [78, 1, 1, "", "find_all_islands"], [78, 1, 1, "", "options_parse"], [78, 1, 1, "", "replace_labels"], [78, 1, 1, "", "sample_img"], [78, 1, 1, "", "sample_nearest_nonzero"], [78, 1, 1, "", "sample_parc"]], "recon_surf.smooth_aparc": [[79, 1, 1, "", "bincount2D_vectorized"], [79, 1, 1, "", "get_adjM"], [79, 1, 1, "", "main"], [79, 1, 1, "", "mode_filter"], [79, 1, 1, "", "options_parse"], [79, 1, 1, "", "smooth_aparc"]], "recon_surf.spherically_project_wrapper": [[80, 1, 1, "", "call"], [80, 1, 1, "", "setup_options"], [80, 1, 1, "", "spherical_wrapper"]]}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "function", "Python function"], "2": ["py", "class", "Python class"], "3": ["py", "method", "Python method"], "4": ["py", "property", "Python property"], "5": ["py", "attribute", "Python attribute"]}, "objtypes": {"0": "py:module", "1": "py:function", "2": "py:class", "3": "py:method", "4": "py:property", "5": "py:attribute"}, "terms": {"": [24, 30, 44, 47, 56, 59, 60, 61, 64, 66, 83, 84, 85, 86, 87, 88, 90, 92, 94, 96, 97, 100, 102, 103, 107, 109, 110, 111], "0": [14, 20, 25, 28, 30, 32, 33, 34, 41, 43, 44, 46, 47, 48, 50, 54, 59, 61, 62, 63, 66, 67, 78, 79, 83, 87, 88, 89, 92, 93, 94, 96, 97, 99, 100, 102, 103, 104, 106, 107, 110, 111], "001": [28, 86, 91, 99, 102, 103], "002": 99, "003": 99, "01": [94, 106], "015": 90, "02": [88, 90, 109], "04": 90, "049": 90, "05": 90, "06": [33, 47], "065": 90, "07": 111, "076": 90, "084": [88, 90, 109], "1": [14, 22, 24, 28, 30, 32, 33, 34, 41, 42, 43, 44, 46, 47, 48, 50, 54, 62, 63, 64, 66, 67, 69, 71, 78, 79, 83, 84, 85, 86, 88, 90, 95, 96, 97, 98, 99, 100, 102, 103, 106, 107, 109, 111], "10": [15, 20, 25, 28, 83, 88, 89, 90, 94, 96, 100, 107, 109, 110, 111], "100": [73, 111], "1000": [28, 34], "101": 100, "1016": [25, 83, 88, 90, 96, 109, 110], "101a": 100, "1024000000": 94, "1030": 103, "10390573": 104, "10390742": 104, "10g": 100, "10min": 100, "11": [89, 94], "110": 67, "11184216": [104, 107], "1162": [83, 88, 96, 107, 109], "117012": [83, 88, 96, 109, 110], "1181": 90, "118933": [83, 88, 96, 109, 110], "1196": 90, "119703": [25, 83, 88, 96, 109], "12": 94, "121": 89, "130": 34, "140": 92, "1402": 90, "140_orig": 92, "1418": 90, "15": 89, "15gb": 89, "16": [32, 86, 87, 89, 100, 106], "172800": 94, "1750814_": 100, "1750814_3": 100, "1750815_": 100, "1750815_1": 100, "1750815_2": 100, "1750815_3": 100, "1750816": 100, "18": 90, "180": 34, "19": [54, 89, 90], "1d": [14, 15], "1e": [33, 47], "1h": 83, "1mm": [33, 34, 46, 83, 88, 96, 103, 110], "1x1x1": [33, 110], "2": [14, 20, 24, 33, 34, 43, 47, 65, 69, 78, 86, 88, 93, 95, 96, 97, 98, 99, 100, 106, 111], "20": [31, 92], "2000": 34, "2004": 97, "2010": 90, "2011": 90, "2012": [88, 90, 109], "2013": 90, "2014": 90, "2016": 94, "2017": 14, "2020": [83, 88, 96, 109, 110], "2022": [25, 54, 83, 88, 96, 109, 110, 111], "2023": [83, 88, 96, 99, 100, 107, 109, 111], "21": [34, 90], "219": [83, 88, 96, 109, 110], "21e31fb5bea5": 104, "21h1": 89, "21h2": 89, "220d": 104, "24": 47, "240min": 100, "249": 90, "251": [83, 88, 96, 109, 110], "255": [33, 62, 67, 86], "256": [33, 42, 65, 105, 106], "256x256x256": [33, 88, 110], "26": 47, "260": 90, "264": [25, 83, 88, 96, 109], "29": 89, "2a3cf0e1a8c5": 104, "2ae5": 104, "2af6da63d5c1414b832c1f606bbd068a": 107, "2d": [15, 41, 42, 79], "2x": 20, "3": [14, 24, 33, 34, 43, 61, 67, 78, 79, 86, 90, 92, 95, 96, 97, 99, 100, 105, 106, 111], "30": [88, 106, 110, 111], "3000": 34, "31": 44, "311": 106, "32": [47, 83, 87, 88, 96, 107, 109, 111], "320": 106, "33": 34, "358": 90, "370": 90, "3d": [33, 34, 45], "3rd": 83, "3t": [86, 87, 88, 90, 94, 98, 100, 110], "4": [43, 44, 67, 68, 71, 78, 84, 86, 88, 90, 94, 95, 97, 99, 100, 102, 103, 107, 109, 111], "40": 92, "4000": 92, "4080": 92, "43": 44, "44": [24, 43], "47b0": 104, "4c83": 104, "4d0e": 104, "5": [15, 24, 34, 43, 47, 83, 90, 92, 95, 96, 97, 103, 105, 107, 110, 111], "50": [34, 67, 97, 105], "5000": 94, "50th": 30, "51": [34, 106], "512000000": 94, "53": 90, "5455": 104, "57": 90, "5t": [88, 98, 110], "5th": 34, "6": [33, 47, 85, 95, 96, 97, 99, 100, 107], "60": [83, 92], "60mm3": 111, "61": [88, 90, 109], "63": 44, "64": [23, 24, 42, 43], "65535": 54, "66": [90, 99], "7": [23, 42, 44, 71, 85, 88, 89, 92, 96, 97, 100, 103, 106, 110], "70": [34, 44], "71": 106, "79": [56, 106], "7mm": [83, 88, 96], "7t": 86, "8": [87, 89, 96, 97, 99, 111], "81": 90, "814d": 104, "853d": 104, "8g": 89, "8gb": [89, 92], "9": [90, 96, 97, 100, 106], "90": 83, "9000": 94, "95": [46, 83, 103, 111], "95mm": 103, "95th": 30, "96": 34, "97": 90, "98mm": 88, "999": [33, 110], "9e0c": 104, "A": [14, 15, 24, 25, 26, 34, 41, 46, 47, 48, 49, 50, 53, 54, 56, 58, 59, 61, 62, 65, 66, 71, 73, 83, 85, 87, 88, 89, 91, 94, 96, 97, 98, 103, 106, 109, 110], "AND": 97, "AS": 97, "AT": 54, "And": [85, 92, 109], "As": [94, 110], "At": 96, "Be": 96, "Being": 84, "But": 96, "By": [14, 30, 56, 59, 86, 88, 94, 99, 102, 103, 107], "FOR": 97, "For": [20, 21, 28, 30, 31, 41, 48, 56, 73, 84, 85, 86, 87, 88, 89, 90, 92, 94, 97, 98, 99, 100, 102, 103, 105, 107, 109, 110, 111], "If": [15, 20, 29, 30, 33, 38, 46, 47, 48, 50, 54, 58, 61, 62, 64, 65, 66, 73, 76, 78, 80, 83, 85, 87, 88, 89, 91, 92, 93, 94, 96, 97, 98, 100, 102, 103, 105, 107, 109, 110, 111], "In": [30, 33, 56, 59, 84, 86, 87, 88, 89, 90, 91, 92, 94, 96, 97, 102, 107, 110], "It": [14, 30, 31, 64, 65, 66, 75, 85, 86, 87, 89, 90, 91, 92, 96, 98, 99, 100, 104, 110], "NOT": [88, 95], "No": [54, 70, 88, 96, 100], "Not": [54, 88, 97, 110], "OF": 97, "OR": [97, 99], "Of": 94, "On": [87, 89, 110], "One": [50, 99, 111], "That": 92, "The": [13, 14, 15, 20, 24, 25, 26, 28, 29, 30, 32, 33, 34, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 54, 57, 58, 59, 61, 62, 63, 64, 65, 66, 67, 68, 70, 71, 73, 78, 80, 81, 83, 84, 85, 86, 87, 88, 89, 90, 91, 94, 96, 97, 98, 99, 100, 102, 103, 106, 107, 110], "Then": 86, "There": [87, 89, 94, 110], "These": [86, 87, 88, 89, 90, 98, 99, 107], "To": [85, 86, 87, 88, 89, 92, 94, 98, 103, 106], "Will": [102, 103, 107, 111], "With": [87, 94, 99, 109, 110], "_": [94, 100], "__arg": 47, "__call": 32, "__call__": [23, 24, 40, 41, 43], "__fn": 50, "__getitem__": 63, "__init__": 46, "__len__": 63, "__pycache__": 61, "_arg": 59, "_arrai": 47, "_arraytyp": 47, "_get_scale_factor": 63, "_globalstat": 47, "_header": 34, "_inttyp": 47, "_numbertyp": 47, "_pad": 32, "_serialexecutor__fn": 50, "_standarized_img": 63, "_t": 50, "_ti": 50, "a423a576": 104, "a_object": 54, "ab": 47, "abil": 28, "abl": [85, 86, 89, 110], "about": [84, 85, 92, 96, 103], "abov": [33, 34, 85, 86, 87, 88, 90, 94, 97, 98, 103, 109], "absolut": [14, 47, 49, 50, 85, 87, 88, 100, 102, 103, 107, 109, 110], "abus": 84, "acceler": 94, "accept": [54, 84, 87, 97, 100, 110], "access": [86, 87, 89, 94, 98], "accord": [21, 34, 53, 73, 89, 92, 99], "accordingli": [21, 31, 85], "account": [33, 84, 85, 86, 92, 94], "accumul": [30, 56, 66], "accur": [83, 88, 90, 96, 109, 110], "accuraci": 96, "achiev": [86, 110], "acknowledg": 95, "acquir": [87, 90, 98], "acquisit": 90, "across": [24, 43, 47, 90, 96, 100], "act": [84, 97], "action": [47, 58, 84, 94], "activ": [16, 43, 61, 88, 89, 99, 102, 103, 107, 109, 110], "actual": [50, 85, 100], "ad": [21, 47, 54, 58, 74, 88, 89, 92, 94], "adam": 106, "adamw": 106, "adapt": [84, 94], "add": [14, 28, 32, 34, 38, 47, 58, 79, 85, 86, 87, 89, 90, 91, 92, 94, 96, 97, 98, 100, 105, 111], "add_argu": [47, 58], "add_background": 54, "add_cereb_wm": 21, "add_measure_pars": 47, "add_plane_flag": 58, "add_text": 47, "add_two_help_messag": 47, "add_usag": 47, "addendum": 97, "addgaussiannois": 32, "addit": [20, 33, 34, 47, 54, 83, 87, 88, 89, 90, 91, 92, 94, 97, 99, 100, 102, 110, 111], "addition": [88, 89, 109, 110], "address": [84, 85, 86, 100], "adefault": 105, "adj": 78, "adjac": [78, 79, 83, 88, 96, 107, 109], "adjaceni": 79, "adjm": 79, "adjust": [28, 33, 66, 87, 92], "admin": 89, "adni": 103, "advanc": [83, 84, 85, 92, 108], "advantag": 90, "advis": [87, 97], "affect": [47, 86, 88, 100], "affin": [13, 14, 21, 33, 34, 47, 60, 66, 68, 69], "affine_info": 34, "after": [13, 24, 42, 43, 47, 54, 59, 61, 87, 89, 90, 91, 92, 94, 96, 98, 99, 100, 103, 106, 110, 111], "afterani": 100, "aftercorr": 100, "ag": [14, 84, 96], "again": [86, 90, 92], "against": [88, 97], "agg": [88, 102, 103, 107], "aggreg": [23, 39, 42, 64, 66, 88, 96, 102, 103, 107, 111], "agnost": 14, "agre": 97, "agreement": [97, 111], "ahmad": 107, "ai": 96, "aim": [85, 99], "al": [14, 25, 83, 88, 90, 96, 109], "algorithm": 111, "alia": 16, "align": [69, 77, 84, 90], "align_aparc_centroid": 77, "align_flip": 69, "align_point": 81, "align_seg": 81, "align_seg_centroid": 69, "all": [14, 15, 18, 20, 30, 34, 46, 47, 50, 54, 59, 61, 66, 70, 71, 78, 79, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 94, 97, 99, 100, 102, 103, 104, 106, 107, 109, 110, 111], "all_col": 71, "all_flag": 58, "all_id": 71, "all_label": 70, "all_merged_label": 47, "all_nam": 71, "all_valu": 70, "alleg": 97, "alloc": [88, 100], "allow": [24, 33, 34, 43, 58, 63, 83, 86, 87, 88, 89, 90, 94, 99, 100, 102, 103, 107], "allow_root": [58, 88, 107], "allows_root": 58, "almost": 87, "alon": 97, "along": [30, 38, 44, 66, 78, 91, 97, 110], "alongsid": 97, "alpha": [39, 68], "alreadi": [30, 33, 34, 38, 47, 54, 56, 85, 86, 87, 88, 89, 90, 94, 102, 103, 105, 107, 110], "also": [15, 21, 28, 44, 47, 54, 58, 61, 65, 70, 73, 85, 86, 87, 88, 89, 90, 91, 92, 94, 96, 98, 99, 100, 103, 107, 109, 110, 111], "alt": 99, "alt_fil": 34, "altern": [34, 47, 83, 86, 87, 90, 100, 102, 103, 106, 110, 111], "alternate_label": 111, "alternate_mean": 111, "alternate_mixing_coeff": 111, "alwai": [33, 47, 50, 61, 85, 88, 94, 96, 102, 103, 110, 111], "am": 85, "amd64": 94, "amdgpu": 94, "among": 86, "amygdala": 96, "an": [13, 14, 15, 20, 25, 28, 33, 34, 47, 48, 49, 50, 54, 56, 58, 61, 65, 66, 67, 70, 72, 78, 79, 84, 86, 87, 88, 89, 90, 91, 92, 94, 96, 97, 99, 106, 107, 110], "analog": 50, "analys": [87, 94, 98], "analysi": [47, 83, 86, 87, 88, 90, 92, 94, 96, 98, 109, 110, 111], "analyz": [33, 34, 46, 86, 87, 90, 102, 103, 110], "anat": [102, 103], "anatom": [34, 83, 90, 91, 110], "anatomi": 90, "angl": 68, "angles2rmat": 68, "ani": [14, 30, 33, 38, 46, 47, 50, 54, 56, 70, 80, 84, 85, 86, 87, 88, 89, 92, 96, 97, 98, 105, 106, 111], "anneal": 28, "annot": [70, 78, 79, 91, 97], "annot_id": 70, "annot_v": 70, "anoth": [54, 70, 85, 86], "answer": 84, "anyth": [102, 103], "apach": [95, 96, 99, 100], "aparc": [34, 38, 58, 69, 77, 79, 86, 87, 88, 91, 92, 96, 102, 103, 105, 110], "aparc_aseg": 103, "aparc_aseg_segfil": [102, 103], "aparc_nam": 38, "aparc_nocc": 38, "aparc_vinn_axial_v2": [103, 104], "aparc_vinn_coronal_v2": 103, "aparc_vinn_sagittal_v2": 103, "aparcdkt": 96, "api": [50, 104], "appear": [84, 97], "append": [34, 70, 71, 87], "appendix": 97, "appl": [88, 94], "appli": [14, 15, 24, 32, 33, 43, 47, 50, 54, 65, 67, 79, 84, 97, 104], "applic": [59, 87, 89, 97], "apply_transform": 14, "apply_warp": [81, 102], "appoint": 84, "approach": [86, 90], "appropri": [84, 89, 97], "approxim": [83, 110], "apt": 89, "ar": [15, 20, 23, 33, 34, 42, 47, 48, 50, 54, 58, 59, 61, 64, 67, 70, 73, 78, 79, 84, 85, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 102, 103, 105, 107, 109, 110], "architectur": [88, 89, 110], "are_all_subject_fil": 50, "area": [65, 91], "arg": [17, 25, 27, 28, 30, 47, 50, 51, 58, 59, 61, 94], "arg_typ": 81, "argpars": [25, 33, 46, 47, 48, 51, 58, 61, 66, 71, 73, 74, 77, 78, 80], "args2cfg": 46, "argument": [25, 27, 33, 34, 38, 46, 47, 48, 50, 51, 58, 61, 66, 80, 87, 91, 94, 95, 98, 99, 100], "argument_pars": 74, "argumentpars": [25, 33, 46, 47, 58, 61, 66], "argumenttypeerror": 48, "aris": 97, "arithmet": [30, 56], "arm": [85, 89], "around": [33, 47, 67, 73, 78, 83, 96], "arr": 20, "arrai": [13, 14, 15, 20, 29, 33, 34, 44, 45, 47, 54, 56, 62, 72, 73, 74, 78, 79, 100], "array_lik": [14, 30, 47], "array_or_tensor": 54, "arraylik": [67, 70, 72, 74, 77, 79], "artefact": 96, "artifact": 14, "as_futur": 59, "asd": 30, "aseg": [16, 21, 34, 35, 38, 58, 67, 69, 74, 86, 87, 88, 91, 92, 96, 102, 103, 105, 110, 111], "aseg_cc": 74, "aseg_data": 45, "aseg_map": 15, "aseg_nam": 103, "aseg_nocc": [34, 103], "asegdkt": [74, 83, 86, 88, 91], "asegdkt_segfil": [44, 50, 83, 87, 88, 95, 102, 103, 110], "ask": [85, 89], "assd": 30, "assert": 97, "assert_no_root": 50, "assertionerror": [65, 66], "assess": 91, "assign": [50, 87, 90, 99, 100], "associ": [14, 40, 47, 50, 54, 61, 97, 100], "assum": [33, 47, 58, 68, 89, 97, 110], "asymmetri": 90, "async_finish": 59, "async_io": [22, 46, 64, 66, 102, 103, 107], "async_save_img": 46, "asynchron": [46, 50, 66, 102, 103, 107], "aten": 89, "atla": [87, 88, 91, 96, 98, 110], "atlas": 110, "atrophi": 90, "attach": 97, "attack": 84, "attent": [77, 84], "attest": 95, "attr_nam": 50, "attribut": [16, 22, 28, 32, 38, 39, 40, 41, 42, 43, 46, 50, 54, 56, 58, 59, 61, 64, 65, 95, 97], "attributeerror": 50, "aug": [54, 106], "augment": [16, 35, 81, 106], "augmentationpadimag": 32, "augmentationrandomcrop": 32, "author": [54, 97, 99, 100, 102, 111], "authorship": 97, "auto": [22, 46, 48, 50, 64, 66, 86, 87, 88, 102, 103, 107, 111], "auto_noccseg": [86, 87, 91, 92, 103, 105], "autodetect": 88, "autom": [83, 88, 96, 107, 109], "automat": [33, 63, 66, 86, 87, 88, 91, 94, 98, 99, 104, 110, 111], "aux_subjects_fil": 19, "auxiliari": 19, "avail": [30, 56, 60, 66, 84, 86, 87, 89, 91, 94, 97, 98, 102, 106, 107, 110], "available_s": 38, "averag": 30, "avoid": [86, 87, 88, 90, 94, 98, 110], "awar": [85, 96, 110], "ax": [30, 62], "axi": [15, 34, 38, 62, 110], "axial": [15, 34, 38, 39, 46, 62, 66, 102, 103, 105, 106, 107], "axial2coron": [15, 62], "axial2sagitt": [15, 62], "aziz": [83, 88, 96, 107, 109], "b": [34, 54, 59, 83, 85, 87, 88, 89, 90, 92, 96, 97, 98, 99, 100, 105, 107, 109, 110], "b2share": [104, 107], "b5b32d45fc59": 104, "bach": 55, "back": [15, 34, 62, 77, 89, 92], "backbon": 46, "background": [14, 29, 30, 44, 67, 106], "bahrami": [25, 83, 88, 96, 107, 109], "balanc": [15, 34], "ball": [67, 78], "ban": 84, "bar": [94, 99], "base": [13, 14, 23, 25, 30, 47, 50, 54, 62, 63, 66, 69, 83, 85, 86, 87, 88, 89, 90, 91, 94, 96, 97, 99, 100, 102, 103, 104, 106, 109, 110, 111], "base_lr": [28, 106], "base_ornt": 62, "base_r": 106, "base_shap": 20, "baseexcept": 50, "baseid": [88, 110], "bash": [89, 94, 100], "bashrc": 89, "basi": [97, 110], "basic": [87, 94], "batch": [15, 22, 24, 29, 39, 40, 42, 43, 46, 57, 66, 88, 96, 100, 102, 103, 106, 107, 108], "batch_dict": 31, "batch_loss": 55, "batch_output": [31, 57], "batch_siz": [39, 46, 65, 66, 88, 102, 103, 106, 107], "bbox": 16, "bbox_3d": 34, "bctx": 94, "becaus": [94, 100, 111], "been": [85, 89, 97], "befor": [59, 86, 94, 98, 99], "beforehand": 88, "behalf": 97, "behavior": [59, 84, 85, 86, 103], "behind": 95, "being": [14, 47, 54, 93, 99], "belong": [47, 87], "below": [33, 34, 86, 87, 88, 89, 91, 92, 97, 103, 105, 110], "benefici": 97, "benefit": [87, 96, 99], "bernal": 90, "bert": 90, "bert_1": 90, "bert_2": 90, "best": [26, 49, 84, 95, 110], "best_metr": [26, 49], "beta": 68, "better": [87, 88, 89, 107, 110], "between": [14, 30, 33, 34, 38, 44, 47, 48, 54, 68, 79, 88, 90, 103], "beyond": 83, "bg_intersect": 44, "bg_label": 44, "bia": [14, 47, 67, 83, 88, 90, 92, 95, 102, 107, 109, 110], "bias_correct": 86, "biasfield": [86, 87, 88, 91, 111], "bicub": 65, "bid": [102, 103], "bigger": [44, 48, 88], "biject": 54, "bilinear": 65, "bill": 94, "billot": 14, "bin": [48, 89], "binar": 78, "binari": [21, 30, 34, 47, 67, 89, 107], "bincount2d_vector": 79, "bind": 97, "biomed": 30, "bit": 92, "bkg": 34, "blank": [15, 20, 34, 38, 61], "blank_slice_thresh": 105, "bleed": [94, 98], "block": [23, 24, 42, 43, 59, 65], "blt": 38, "blue": [31, 57], "blur_factor": 14, "bn": [24, 43], "bn0": 43, "bodi": 84, "bonu": 92, "bool": [15, 19, 26, 33, 34, 38, 39, 44, 47, 49, 50, 54, 56, 61, 62, 66, 69, 70, 71, 76, 79], "boolean": 15, "bootstrap": 94, "border": [20, 38, 47, 105], "border_patch": 47, "both": [13, 47, 56, 64, 84, 88, 89, 90, 94, 99, 100, 107, 109, 110], "bottleneck": 42, "bottom_left": 65, "bottom_right": 65, "bound": [20, 34], "boundari": [15, 78, 79, 111], "bounding_volume_offset": 20, "box": 34, "br": [47, 111], "brain": [14, 46, 67, 83, 86, 87, 88, 89, 91, 92, 96, 103, 107, 109, 110], "brain_seg": 16, "brainmask": [86, 88, 91, 92, 103, 110], "brainmask_nam": [58, 103], "brainseg": 111, "brainsegnotv": 111, "brainsegnotventsurf": 111, "brainsegvol": 111, "brainstem": [21, 96], "brainvol": 111, "brainvolstat": 47, "branch": [61, 85, 87, 88, 89], "break": [47, 89], "bretel": [83, 88, 96, 107, 109], "brew": 89, "broken": [87, 89], "brun_fastsurf": [87, 90, 100, 108, 110], "brun_subject": 87, "buckner_data": 92, "budget": 100, "buffer": 39, "bug": 95, "build": [23, 28, 42, 61, 65, 70, 83, 87, 88, 89, 92, 95, 96, 109, 110], "build_annot": 70, "build_cach": 61, "build_fil": 61, "build_model": [23, 42, 65], "builder": 94, "buildkitd": 94, "buildx": 94, "built": [89, 94], "builtin": [50, 99], "bundl": 89, "byte": 50, "c": [33, 41, 42, 43, 83, 89, 97], "c6cf7bc6": 104, "ca": [89, 94], "cach": 61, "cachemount": 94, "calcul": [26, 30, 41, 46, 47, 49, 56, 83, 88, 102, 111], "calculate_flip_orient": 62, "calculate_merged_label": 47, "call": [32, 58, 80, 87, 89, 90, 92, 98, 100, 102, 103, 106, 107, 110], "callabl": [30, 50, 56, 58], "callosum": [34, 38, 74, 87, 91, 92, 105], "can": [14, 20, 30, 33, 34, 41, 44, 48, 50, 54, 56, 58, 61, 65, 66, 70, 73, 78, 79, 85, 87, 88, 89, 90, 92, 93, 94, 95, 96, 98, 99, 100, 102, 103, 104, 106, 107, 110, 111], "can_resolve_attribut": 50, "can_resolve_filenam": 50, "canaddargu": 58, "candid": 21, "candidate_lbl": 21, "cannot": [94, 97, 99, 111], "cap": [34, 89], "capabl": 99, "care": [70, 87, 94], "carefulli": [85, 86], "carol": 14, "carri": 97, "case": [25, 30, 33, 56, 59, 71, 73, 85, 86, 87, 88, 89, 92, 94, 96, 98, 99, 100, 110], "case_bias_correct": 86, "case_bias_onli": 86, "case_with_edit": 86, "cast": 39, "catch": 46, "categor": 56, "caus": [50, 66, 86, 94, 97, 98], "cc": [74, 86], "ccomput": 24, "cd": [85, 87, 89, 92, 98, 100], "ce": 41, "cell": 92, "center": [20, 65, 67], "centroid": [67, 69, 77], "centroids_dst": 69, "centroids_mov": 69, "cereb": [21, 83], "cereb_segfil": [88, 102], "cereb_statsfil": 102, "cereb_subseg": [15, 20, 21], "cereb_subseg_lateral_mask": 21, "cerebdataset": 16, "cerebellar": [21, 83, 102], "cerebellum": [15, 25, 83, 88, 91, 92, 96, 102, 109], "cerebnet": [81, 83, 88, 89, 95, 96, 101, 104, 108, 109], "cerebnet_axial_v1": 102, "cerebnet_coronal_v1": 102, "cerebnet_model": 81, "cerebnet_sagittal_v1": 102, "cerebnetdataset": 18, "cerebr": 34, "cerebralwhitematt": 111, "cert": 94, "certain": [102, 103, 107, 110, 111], "certif": [89, 94], "cfg": [14, 16, 17, 18, 19, 22, 26, 28, 29, 31, 35, 36, 39, 41, 42, 46, 49, 53, 55, 57, 63, 64, 65, 66, 106], "cfg_": 58, "cfg_ax": [46, 66, 103, 107], "cfg_cor": [46, 66, 103, 107], "cfg_file": [46, 51, 106], "cfg_sag": [46, 66, 103, 107], "cfgnode": [26, 31, 36, 39, 41, 42, 46, 49, 51, 53, 57, 64, 65, 66], "chain": 54, "challeng": 30, "chan": [83, 96], "chang": [54, 81, 85, 86, 87, 88, 89, 90, 94, 97, 98, 103, 106, 109, 110, 111], "channel": [15, 40, 106], "charact": [47, 97], "characterist": 84, "charg": 97, "check": [26, 33, 34, 44, 47, 48, 49, 50, 54, 66, 85, 86, 88, 89, 96, 100, 102, 103, 104, 107, 110], "check_affine_in_nifti": 33, "check_and_download_ckpt": 49, "check_dtyp": 33, "check_path": 57, "check_shape_affin": 47, "check_volum": 44, "checkout": [85, 94], "checkpoint": [39, 46, 58, 61, 64, 66, 81, 88, 89, 100, 102, 104], "checkpoint_dir": [26, 49], "checkpoint_nam": 49, "checkpoint_path": [26, 49], "checkpointconfigdict": 49, "chiasma": 34, "chip": [88, 89, 94], "chmod": 89, "choic": [88, 105, 107, 109, 111], "choos": [97, 103], "choroid": 44, "chosen": 86, "chunk": 50, "chunksiz": 50, "circumst": 84, "cite": [83, 88, 96, 107, 109, 110], "ckpt": [39, 46, 49, 64, 107], "ckpt_": 58, "ckpt_ax": [46, 66, 102, 103, 107], "ckpt_cor": [46, 66, 102, 103, 107], "ckpt_dir": [26, 49], "ckpt_sag": [46, 66, 102, 103, 107], "claim": 97, "clarifi": 84, "class": [14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 46, 47, 49, 50, 54, 55, 56, 57, 58, 59, 61, 63, 64, 65, 81, 83, 106], "class_id": 30, "class_idx": 30, "class_list": 14, "class_nam": [29, 55], "class_wise_weight": 15, "classes_list": 14, "classif": [24, 42, 43], "classifi": [24, 26, 42, 43, 49, 65], "classifierblock": [24, 43, 65], "classmethod": 54, "classname_to_id": 29, "clean": [34, 103], "clean_cortex_label": 34, "cleanup": [87, 100], "clear": [85, 96], "cli": 94, "clinic": 96, "clone": [85, 87, 89], "close": [34, 61], "closest": [34, 73, 78], "cloud": 92, "cluster": [95, 100, 110], "cm": [31, 56, 57], "cmap": [31, 57], "cmax": 34, "cmdf": 85, "cmin": 34, "cmp_dtype": 47, "cnf": 56, "cnf_mat": 56, "cnn": [42, 87], "co": [83, 85, 88, 91, 96, 107, 109, 110], "code": [34, 47, 59, 80, 89, 95, 97, 100, 103, 106, 107], "code_1": 80, "coeffici": [30, 56, 111], "col": 70, "col_id": 70, "colab": 95, "colappend": 71, "collab": 92, "collect": 85, "colnam": 71, "colon": [87, 94, 98, 110], "color": [31, 34, 38, 54, 57, 70, 71, 78, 103, 105], "color_palett": 54, "colorlookupt": 54, "colorlut": [34, 47], "colormap": [54, 92], "colormapregistri": 57, "colort": [70, 71], "colortab": 70, "colortab_nam": 70, "colour": [57, 70], "column": [47, 105], "com": [14, 85, 87, 89, 90, 94], "combi": [34, 105], "combin": [24, 28, 34, 41, 43, 70, 88, 90, 97, 105, 111], "combinedloss": 41, "come": [87, 92], "comma": [47, 100], "command": [25, 33, 44, 45, 47, 61, 66, 67, 69, 70, 71, 73, 74, 75, 76, 77, 78, 79, 80, 85, 86, 87, 88, 89, 90, 92, 94, 98, 99, 109, 110, 112], "command1": 80, "command2": 80, "commandlin": [47, 89, 112], "comment": [84, 85], "commerci": 97, "commit": [84, 85], "common": [81, 84, 97, 102, 103, 107], "commonli": 30, "commun": [84, 85, 86, 97], "compar": [30, 33, 86, 90, 96, 107], "compat": [47, 66, 83, 96, 100, 111], "competit": [23, 24, 42, 43], "competitivedecoderblock": [24, 43], "competitivedenseblock": [24, 43], "competitivedenseblockinput": [24, 43], "competitivedensedecod": [24, 43], "competitiveencoderblock": [24, 43], "competitiveencoderblockinput": [24, 43], "compil": [85, 97], "complaint": 84, "complet": [34, 80, 85, 88], "compli": [88, 97], "compon": [16, 21, 30, 34, 56, 78, 85, 89, 103], "compress_out_spac": 54, "compris": [24, 43, 86], "comput": [14, 23, 24, 29, 30, 33, 39, 44, 47, 56, 62, 64, 67, 78, 85, 86, 87, 92, 94, 96, 97, 98, 110, 111], "comput_dice_cnf": 56, "compute_dsc": 56, "concaten": 61, "concatenation": [23, 42], "concern": 91, "concurr": [34, 46, 47, 59], "conda": 61, "condit": [33, 97, 111], "conduct": 95, "conf": 88, "conf_nam": [50, 58, 102, 103], "confidenti": 84, "config": [26, 28, 31, 36, 39, 41, 42, 46, 49, 51, 53, 57, 58, 64, 65, 66, 94, 102, 105, 106, 107], "config_fil": 27, "configtyp": [49, 58], "configur": [25, 26, 31, 36, 39, 41, 46, 47, 49, 51, 53, 57, 64, 65, 66, 85, 94, 97, 106, 111], "conflict": [85, 89, 94], "conform": [34, 46, 50, 81, 86, 87, 88, 91, 102, 103, 110], "conform_and_save_orig": 46, "conform_min": 34, "conform_to_1mm_threshold": [33, 46, 103], "conform_vox_s": 33, "conformed_img_s": 33, "conformed_nam": [87, 88, 102, 103], "conformed_t1_fil": 50, "conformed_t1_output": 110, "conformed_vox_s": 33, "confus": [29, 31, 55, 56, 57], "conjeti": [83, 88, 96, 109, 110], "connect": [16, 23, 24, 30, 34, 42, 43, 47], "consecut": 54, "consequenti": 97, "consid": [14, 30, 33, 47, 70, 78, 81, 84, 85, 86, 88, 100, 102, 103, 107], "consist": [24, 83, 88, 89, 90, 97, 110], "consol": [87, 99, 110], "conspicu": 97, "constitut": 97, "constrain": [47, 90], "constru": 97, "construct": [46, 84, 90, 100], "construct_adj_clust": 78, "constructor": 80, "contact": 84, "contain": [14, 15, 20, 29, 30, 34, 39, 41, 44, 47, 50, 54, 56, 57, 58, 59, 61, 64, 65, 66, 70, 78, 83, 87, 88, 89, 90, 91, 92, 94, 97, 98, 99, 100, 103, 106, 110], "containerd": 94, "content": [49, 59, 61, 97], "context": [85, 94], "continu": [15, 70, 85, 89], "continuum": 89, "contract": 97, "contrari": 103, "contrast": 14, "contribut": [14, 84, 86, 93, 95, 97], "contributor": [95, 96, 97], "contributori": 97, "control": [86, 87, 88, 92, 97, 99, 107, 110], "conv": [24, 43], "conv0": 43, "conv1": 43, "conv2": 43, "conv3": 43, "conveni": [59, 86, 92], "convent": 50, "converg": 67, "convers": [97, 98], "convert": [14, 30, 32, 34, 47, 48, 54, 66, 68, 92, 98], "convinc": 85, "convolut": [23, 24, 42, 43, 106], "coord": [69, 73], "coordin": [19, 34, 67, 73, 78], "copi": [50, 74, 86, 92, 97, 100], "copy_orig_nam": 50, "copy_orig_t1_fil": 50, "copyright": 97, "core": [83, 87, 88, 99], "coreg": [66, 88, 107], "corner": 47, "coron": [15, 34, 39, 46, 62, 66, 102, 103, 105, 106, 107], "coronal2axi": [15, 34], "coronal2sagitt": [15, 34], "corpu": [34, 38, 74, 87, 91, 92, 105], "correct": [21, 34, 35, 47, 63, 67, 73, 75, 76, 83, 84, 87, 88, 89, 90, 91, 92, 95, 96, 102, 103, 107, 109, 110, 111], "correct_cereb_brainstem": 21, "correctli": [33, 75, 92, 94], "correspond": [13, 14, 15, 24, 34, 43, 44, 50, 54, 66, 70, 73, 78, 79, 86, 88, 90, 91, 96, 110], "cortex": [34, 38, 70, 78, 79, 86, 91, 105, 110, 111], "cortex_border_mask": 34, "cortex_label_nam": 70, "cortex_mask": 34, "cortex_stop": 34, "cortic": [34, 69, 78, 83, 86, 90, 91, 92, 96, 110], "cosin": 28, "cosineannealingwarmrestart": 53, "cosineannealingwarmrestartsdecai": 28, "cosinelr": 28, "cosinewarmrestart": 106, "could": [84, 87, 89], "count": [47, 60, 79, 87], "counterclaim": 97, "coupl": [89, 92], "cours": 90, "coven": 95, "cover": [33, 85, 92], "cpu": [50, 60, 87, 88, 92, 96, 98, 99, 100, 102, 103, 107, 110, 111], "cpu_onli": 100, "cpu_partit": 87, "cr": 86, "creat": [15, 17, 21, 26, 33, 34, 36, 38, 45, 46, 47, 49, 50, 54, 57, 66, 70, 71, 73, 74, 75, 76, 77, 78, 79, 80, 84, 85, 87, 88, 89, 90, 91, 92, 94, 96, 98, 99, 102, 103, 107, 109, 110, 111], "create_annot": 81, "create_checkpoint_dir": [26, 49], "create_hdf5_dataset": [18, 38], "create_mask": 45, "create_weight_mask": 34, "create_weight_mask2d": 15, "creation": [87, 88, 89, 95, 105, 107, 110], "criteria": 33, "critic": [84, 85], "crop": [13, 20, 32, 33, 40, 42, 47, 65], "crop_patch_to_mask": 47, "crop_posit": [40, 42, 65], "crop_transform": 20, "crop_typ": 32, "cross": [23, 41, 42, 55, 78, 88, 90, 97, 110], "cross_entropy_loss": 41, "crossentropi": 41, "crossentropy2d": 41, "csc_matrix": 78, "csf": 34, "csr": 79, "csr_matrix": 79, "csv": [100, 102, 103, 105], "csv_file": [58, 102, 103, 105], "ctrl": 99, "ctx": [34, 105], "ctx_thresh": 34, "cube": [33, 75, 88, 110], "cubic": [33, 34], "cuda": [30, 43, 50, 56, 88, 89, 94, 99, 102, 103, 107, 111], "cur_epoch": [26, 28, 29, 55], "cur_it": [29, 55], "curl": [89, 92], "curr_it": 28, "current": [26, 28, 29, 46, 47, 49, 50, 54, 55, 70, 85, 88, 93, 94, 98, 100, 102], "current_plan": 46, "current_subject": 19, "curv": 91, "curvatur": 91, "custom": [89, 94, 98, 110], "custom_config": 106, "customari": 97, "cwd": [98, 99], "cyclic": 90, "d": [25, 83, 85, 87, 88, 94, 96, 97, 99, 109, 110], "d9e37247": 104, "d_1": 20, "d_2": 20, "d_n": 20, "daemon": [94, 98], "damag": [96, 97], "dat": 86, "data": [13, 15, 17, 19, 20, 21, 22, 28, 30, 33, 34, 36, 39, 40, 42, 43, 45, 46, 47, 48, 54, 57, 58, 62, 63, 64, 66, 75, 78, 86, 87, 88, 89, 91, 92, 94, 95, 96, 98, 99, 100, 103, 105, 107, 110, 112], "data2": 34, "data_cfg": 16, "data_dict": [15, 20], "data_dir": 105, "data_inseg": 45, "data_load": [38, 57, 81, 105, 110], "data_path": 38, "data_set_s": 38, "data_util": 81, "datadir": [87, 110], "datafram": [34, 38, 47, 54], "dataload": [17, 36, 39, 57, 64, 81, 106], "dataset": [14, 17, 36, 38, 64, 81, 86, 89, 94, 105, 106], "dataset_nam": [18, 38], "dataset_path": [16, 35], "datatyp": 48, "datautil": 34, "date": [54, 71, 87, 97, 99, 100, 111], "david": [54, 99, 100, 107, 111], "de": [34, 84, 99, 100, 104, 107], "deactiv": [83, 88, 107], "debug": [47, 87, 99, 108], "dec": 111, "decai": 28, "decay_base_lr": 28, "decid": 89, "decis": [88, 96, 102, 103, 107], "decod": [24, 42, 43], "decode1": 42, "decode2": 42, "decode3": 42, "decode4": 42, "decoder_output1": 42, "dedic": [90, 96, 110], "deem": 84, "deep": [25, 34, 58, 74, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 96, 99, 100, 102, 103, 107, 109, 110], "deep_sulci_and_wm_strand_mask": 34, "deepmi": [87, 89, 92, 94, 98, 110], "default": [14, 15, 19, 20, 26, 28, 30, 31, 33, 34, 38, 39, 41, 42, 44, 46, 47, 49, 50, 54, 55, 56, 57, 58, 59, 60, 61, 62, 64, 65, 66, 67, 69, 70, 71, 73, 77, 78, 79, 83, 86, 87, 88, 89, 94, 96, 98, 100, 102, 103, 104, 105, 109, 110, 111, 112], "default_criteria": 33, "default_devic": 39, "defaults_path": 58, "defend": 97, "defin": [20, 24, 30, 34, 43, 44, 47, 50, 56, 64, 79, 84, 86, 87, 88, 90, 94, 97, 99, 100, 102, 103, 106, 107, 110, 111], "definit": [23, 42, 88, 91, 97, 102, 103], "deform": 102, "degre": 68, "deleg": 99, "delet": 85, "deliber": 97, "delimit": [87, 100], "delin": 83, "delta": 86, "dens": [23, 24, 42, 43], "depend": [61, 85, 86, 87, 93, 94, 100, 110, 111], "depth": 13, "deriv": [20, 86, 88, 96, 97], "derogatori": 84, "describ": [25, 47, 58, 61, 66, 85, 89, 90, 92, 97], "descript": [85, 91, 93], "descriptor": 48, "design": 97, "desir": [34, 39, 44, 50], "desktop": [89, 94], "dest": 58, "destin": [68, 72, 77, 79], "detach": 94, "detail": [25, 28, 33, 47, 83, 84, 85, 86, 87, 88, 89, 92, 94, 96, 109], "detect": [50, 86, 87, 88, 90, 94, 99], "determin": [28, 30, 33, 34, 60, 61, 62, 63, 70, 79, 84, 85, 88, 94, 97, 103], "deubg": 31, "dev": [85, 87, 88, 89, 94, 110], "develop": [81, 85, 87, 94, 96, 110], "deviat": [14, 32, 33], "devic": [22, 29, 30, 39, 43, 46, 50, 55, 56, 58, 64, 66, 87, 88, 89, 94, 96, 99, 102, 103, 107, 111], "device_num": [88, 103], "dice": [23, 29, 30, 41, 42, 55, 56], "dice_loss": 41, "dice_scor": [29, 30, 56], "diceloss": 41, "dicescor": [30, 56], "dict": [15, 16, 19, 20, 29, 38, 39, 43, 44, 46, 47, 49, 50, 54, 58, 63, 72], "dictionari": [15, 19, 20, 29, 34, 38, 44, 47, 49, 54, 58, 61, 64, 66], "did": [94, 100, 110], "dier": [83, 88, 90, 96, 109, 110], "dieseas": 96, "differ": [33, 39, 50, 66, 84, 86, 87, 88, 89, 90, 94, 96, 97, 99, 109, 110, 111], "digit": [47, 94, 111], "dilat": [34, 44, 45, 103], "dilshad": 107, "dim": 20, "dimens": [13, 15, 20, 30, 33, 42, 66, 106, 110], "dimension": [20, 34, 40, 67], "dir": [26, 49, 61, 70, 88, 99, 107, 109, 110], "direct": [15, 33, 62, 78, 86, 88, 89, 90, 97, 98, 102, 107], "directli": [87, 88, 94, 96, 99, 102, 103, 107, 110, 111], "director": 70, "directori": [13, 18, 26, 38, 46, 47, 49, 50, 58, 61, 66, 70, 85, 86, 87, 88, 89, 90, 91, 92, 94, 98, 100, 102, 105, 106, 107, 109, 110, 111], "disabl": [55, 84, 88, 99, 110], "disable_confusion_mat": 55, "discard": 105, "disclaim": 97, "disconnect": [21, 45, 78], "disconnetct": 78, "discourag": [87, 94], "discriminator_block": 24, "discuss": 97, "diseas": 90, "disk": 73, "displai": [33, 92, 97], "distanc": [30, 73, 78], "distort": 86, "distribut": [30, 34, 39, 56, 87, 89, 97, 100], "distro": 89, "div": 47, "diverg": 85, "divid": 47, "divis": 92, "dkm": 94, "dkt": [69, 74, 87, 88, 91, 96, 110], "dktatla": [34, 58, 83, 86, 87, 88, 91, 92, 102, 103, 105, 110], "dl": [88, 102, 103, 110], "dnum": 45, "do": [33, 38, 47, 66, 84, 87, 88, 89, 90, 92, 94, 95, 97, 98, 100, 102, 103, 105, 107, 109, 110, 111], "doc": [28, 89, 94], "docker": [90, 95, 96, 98, 99], "docker_buildkit": 94, "dockerfil": 94, "dockerhub": [87, 89, 95, 98, 110], "document": [28, 61, 85, 87, 89, 91, 94, 96, 97, 99, 100, 109], "doe": [20, 33, 34, 47, 49, 58, 61, 74, 87, 88, 90, 94, 96, 97, 99, 100, 102, 103, 107, 110, 111], "doesn": 14, "doi": [25, 83, 88, 90, 96, 107, 109, 110], "don": [89, 92, 110], "done": [33, 62, 88, 89, 90, 99, 100, 102, 103, 107], "dot": 111, "doubl": 100, "down": 96, "download": [49, 66, 89, 92, 94, 104], "download_checkpoint": [49, 81, 89, 108, 112], "downsampl": 42, "downstream": [86, 90, 91, 95], "draw": 50, "dri": [89, 94], "driver": [89, 94], "drop": [21, 26, 34, 49, 71, 87, 110, 111], "drop_classifi": [26, 49], "drop_disconnected_compon": 21, "drop_unknown": 71, "drug": 90, "dry": [87, 100], "dry_run": [59, 94], "dsc": 56, "dst": 69, "dst_fname": 72, "dst_header": 72, "dst_max": 33, "dst_min": 33, "dtype": [15, 33, 34, 46, 48], "dtypelik": [34, 47], "due": [89, 96], "dummi": 50, "dura": 86, "dure": [14, 55, 63, 86, 89, 104, 106, 109], "dx": [83, 88, 96, 109, 110], "dzne": [84, 94, 99, 100, 107], "dzne_manu": 21, "e": [21, 25, 30, 33, 34, 47, 48, 50, 56, 61, 69, 70, 73, 75, 83, 84, 85, 86, 87, 88, 90, 91, 93, 94, 96, 98, 99, 100, 102, 103, 104, 105, 107, 109, 110, 111], "each": [14, 15, 20, 21, 29, 30, 34, 42, 45, 47, 56, 58, 66, 73, 78, 79, 88, 90, 97, 99, 100, 109, 110], "earli": 90, "earlier": 91, "easili": [89, 98], "echo": [89, 100], "edg": [15, 32, 34, 38, 78, 79, 105], "edge_w": 105, "edge_weight": 38, "edit": [84, 88, 89, 94, 95, 110], "editori": 97, "edu": [86, 87, 88, 92, 98, 110], "educ": [83, 84, 96], "effect": [34, 47, 54, 83, 90, 95, 111], "effici": [20, 47, 89, 94, 100], "either": [20, 32, 33, 34, 39, 41, 47, 49, 59, 61, 73, 85, 90, 92, 97, 100, 103, 111], "elabor": 97, "electron": [84, 97], "element": [15, 20, 29, 30, 34, 38, 50, 66, 78, 102, 103, 105, 107, 111], "els": [20, 30, 76, 85, 102, 103, 107], "emad": 107, "email": [89, 100, 102], "empathi": 84, "emphas": 15, "emploi": 83, "empti": [47, 54, 61, 78, 87, 88, 94, 98, 100, 111], "emul": 89, "en": 94, "enabl": [14, 55, 88, 89, 96, 99, 102, 106, 107, 110], "enable_confusion_mat": 55, "encod": [24, 42, 43], "encode1": 42, "encode2": 42, "encode3": 42, "encode4": 42, "encourag": [85, 90], "end": [24, 29, 33, 43, 47, 79, 86, 87, 99, 100], "end_sect": 47, "enforc": [33, 90, 95], "engin": [30, 56], "enhanc": 95, "enough": [88, 89, 90, 102, 103, 107, 110], "ensur": [85, 110], "entir": 107, "entiti": 97, "entri": [34, 47, 50, 54, 58, 61, 90, 94], "entropi": [23, 41, 42, 55], "entrypoint": [87, 94, 110], "enum": [33, 45], "enumer": [33, 86], "env": [88, 89, 99, 109, 110], "environ": [84, 85, 87, 88, 94, 98, 99, 109], "ep": [33, 47], "epoch": [26, 28, 29, 49, 55, 106], "epsilon": [33, 47], "equal": [30, 47, 48, 64, 70, 78, 88], "equival": [33, 87, 88, 91, 98, 102, 103, 107, 110, 111], "erod": [34, 103], "eros": [34, 45], "err": 59, "err_str": 59, "error": [34, 47, 50, 61, 66, 75, 85, 86, 96], "especi": [86, 87], "estim": [14, 44, 86, 87, 88, 90, 91, 92, 96, 109, 110], "estimatedtotalintracranialvol": 111, "estrada": [83, 88, 96, 107, 109, 110], "et": [14, 25, 83, 88, 90, 96, 109], "eta_min": 28, "etc": [47, 50, 88, 90, 93, 94, 96, 100, 110, 111], "ethnic": 84, "etiv": [86, 87, 88, 110, 111], "eudat": 107, "eval": [19, 39, 64], "evalu": [14, 39, 47, 64, 102, 107, 111], "even": [86, 87, 89, 90, 97], "event": [84, 90, 97], "everi": 89, "everyon": 84, "everyth": 89, "everywher": 30, "evolv": 90, "exact": 111, "exactli": [33, 47], "exampl": [30, 34, 56, 78, 84, 86, 88, 89, 90, 92, 95, 96, 97, 98, 99, 100, 107, 111, 112], "except": [25, 46, 50, 87, 90, 94, 97, 99, 109], "excit": 96, "exclud": [47, 61, 86, 87, 89, 97, 98, 111], "exclude_id": 47, "excludeid": 111, "exclus": [79, 97, 111], "exec": [87, 90, 92, 94, 98, 99, 100, 110], "execut": [25, 50, 58, 87, 88, 92, 94, 97, 98, 99], "executor": [46, 47, 50, 59], "exercis": 97, "exist": [26, 33, 47, 49, 50, 54, 66, 70, 85, 86, 87, 88, 90, 94, 98, 102, 103, 105, 107, 110, 111], "exit": [88, 100], "expand": 54, "expect": [29, 30, 47, 56, 84, 85, 86, 93, 99, 100, 111], "experi": [26, 31, 49, 57, 84, 92], "experienc": [85, 95], "experiment": [83, 88, 90, 103], "expert": [88, 95, 110], "explain": [85, 89, 94], "explicit": 84, "explicitli": [34, 47, 88, 97, 111], "export": [86, 87, 88, 89, 90, 109, 110], "expr_dir": [26, 49], "expr_num": [26, 31, 49], "express": [84, 97], "ext": 88, "extend": [28, 54, 65, 86, 92], "extens": [59, 71, 98], "exterior": 34, "extern": [86, 88, 100, 107], "extra": 100, "extra_head": 47, "extra_singularity_opt": 100, "extra_singularity_options_seg": 100, "extra_singularity_options_surf": 100, "extract": [33, 34, 46, 47, 58, 61, 68, 69, 86, 90, 96], "exvivo": 70, "f": [70, 73, 78, 85, 88, 89, 90, 98, 110], "f_high": 33, "f_low": 33, "faber": [25, 83, 88, 96, 109], "face": [47, 84], "fact": 111, "factor": [28, 33, 38, 39, 42, 47, 63, 64, 65, 67], "fail": [34, 80, 86, 88, 89, 99, 100, 102, 103, 107], "failur": [25, 60, 66, 97, 100], "fair": 84, "faith": 84, "fall": 89, "fallback": [80, 89], "fals": [15, 18, 19, 20, 22, 24, 26, 30, 33, 34, 35, 43, 46, 47, 49, 54, 56, 61, 62, 64, 66, 69, 102, 103, 104, 105, 107, 111], "faq": 84, "far": [26, 49], "fast": [25, 47, 83, 85, 88, 89, 92, 96, 100, 109, 110], "faster": [88, 89, 94, 96, 110, 111], "fastsurf": [42, 46, 49, 58, 61, 62, 63, 66, 86, 90, 91, 93, 95, 99, 100, 102, 103, 104, 106, 108, 109, 110], "fastsurfer_": 89, "fastsurfer_colorlut": [103, 105], "fastsurfer_hom": [58, 86, 88, 90, 99, 109], "fastsurfer_reconsurf": 89, "fastsurfer_root": 107, "fastsurfercnn": [23, 81, 89, 92, 94, 101, 108, 110, 112], "fastsurfercnnbas": [42, 65], "fastsurferdir": [87, 105], "fastsurferroot": 94, "fastsurfervinn": [42, 83, 87, 88, 89, 96, 109, 110, 112], "fastsurfervinn_axi": 103, "fastsurfervinn_coron": 103, "fastsurfervinn_sagitt": 103, "featur": [24, 43, 85, 94, 96], "feder": [83, 96], "fee": 97, "feed": [34, 43], "feedforward": [41, 42, 43], "feel": 96, "fepegar": 14, "fetch": 85, "few": [89, 90, 92, 96], "fi": 100, "field": [13, 14, 33, 47, 58, 67, 72, 83, 88, 92, 95, 96, 100, 102, 107, 110], "fifth": 99, "fifti": 97, "fig": [31, 57], "figsiz": 31, "figur": [31, 57], "file": [13, 16, 18, 20, 31, 34, 35, 38, 39, 44, 46, 47, 49, 50, 51, 58, 61, 64, 66, 67, 70, 72, 73, 75, 78, 79, 85, 86, 87, 88, 89, 90, 92, 94, 95, 96, 97, 98, 99, 100, 102, 103, 104, 105, 106, 110, 111], "file_or_buff": 54, "file_save_nam": [31, 57], "fileexists_by_attribut": 50, "fileexists_in_subject_fold": 50, "filenam": [26, 39, 46, 49, 50, 58, 67, 70, 72, 73, 75, 78, 88, 91, 92, 99, 110], "filename1": 34, "filename2": 34, "filename_by_attribut": 50, "filename_in_subject_fold": 50, "filepath": [50, 51, 73, 79], "filesystem": 100, "fill": [21, 33, 47, 61, 75, 79, 86, 105], "fill_unknown_labels_per_hemi": 34, "filling_unknown_label": 21, "fillonlylabel": 79, "fillval": 47, "filter": [15, 20, 23, 34, 42, 47, 61, 79, 94, 106], "filter_blank_slic": 105, "filter_blank_slices_thick": [15, 20, 34], "filter_git_statu": 61, "filter_s": 47, "final": [63, 65, 66, 81, 86, 89, 94, 95, 103, 105, 109], "finalsurf": [86, 88, 110], "find": [16, 20, 21, 26, 31, 33, 34, 47, 49, 50, 54, 57, 67, 68, 70, 73, 78, 85, 87, 89, 90, 92, 100, 109, 110], "find_affin": 68, "find_all_island": 78, "find_devic": 50, "find_img_size_by_fov": 33, "find_latest_experi": 57, "find_min_s": 33, "find_rigid": 68, "find_rot": 68, "fine": [26, 49, 88, 91, 94, 110], "fine_tun": [26, 49], "finish": [46, 59, 87, 90, 94, 99, 100], "first": [14, 29, 33, 47, 54, 65, 67, 78, 79, 80, 83, 86, 88, 89, 92, 96, 98, 99, 100, 102, 103, 104, 109, 110, 111], "fischl": [83, 88, 90, 96, 109, 110], "fit": [47, 85, 87, 97], "five": 40, "fix": [73, 75, 76, 85, 86, 89], "flag": [34, 47, 50, 54, 58, 62, 75, 86, 89, 90, 95, 99, 100, 103, 109], "flag_nam": 50, "flex": 42, "flexibl": 90, "flip": [14, 15, 45, 62, 69], "flip_data": 45, "flip_wm_island": 45, "float": [15, 28, 29, 30, 33, 34, 39, 41, 44, 46, 47, 48, 50, 56, 59, 63, 64, 66, 67, 68, 69, 77, 78, 111], "float_gt_zero_and_le_on": 48, "floattensor": 41, "flow": 63, "fly": 89, "fn": [50, 56], "fname": 67, "focus": 84, "folder": [50, 87, 91, 94, 98, 99, 100], "follow": [28, 34, 50, 58, 66, 83, 84, 85, 86, 87, 88, 89, 90, 91, 94, 96, 97, 98, 100, 103, 106, 107, 109, 110, 111], "forc": [33, 47, 59, 85, 88, 103], "force_img_s": 33, "force_iso_vox": 33, "force_lia": 33, "force_lia_strict": 33, "forget": [87, 110], "fork": 85, "form": [30, 56, 97], "format": [33, 34, 35, 47, 61, 63, 67, 68, 72, 73, 90, 92, 98, 99, 100], "format_paramet": 47, "formatt": 47, "formula": 47, "fornix": 83, "forward": [23, 24, 41, 42, 43, 54, 65, 85], "foster": 84, "found": [49, 78, 86, 87, 100, 102, 103, 106, 110], "four": [40, 44, 99], "fp": 56, "fraction": [47, 111], "frame": 34, "free": [84, 87, 88, 96, 97, 98, 110], "freedom": 90, "freesurf": [21, 33, 34, 47, 68, 71, 83, 87, 88, 90, 91, 92, 94, 95, 98, 100, 102, 103, 105, 107, 110, 111], "freesurfer_hom": [86, 87, 88, 89, 90, 110], "freesurfercolorlut": [44, 47], "freeview": [86, 91, 92], "frequenc": [15, 31, 34, 38, 105], "from": [14, 15, 20, 21, 24, 26, 28, 31, 33, 34, 39, 43, 46, 47, 49, 50, 54, 57, 58, 61, 62, 64, 65, 66, 67, 68, 69, 70, 73, 78, 84, 85, 86, 87, 88, 89, 90, 91, 95, 96, 97, 98, 99, 100, 102, 103, 107, 110, 111], "from_seg": 111, "front_top_left": 40, "frozenset": 33, "fs60": 103, "fs_balabel": 81, "fs_licens": [86, 87, 88, 89, 90, 94, 98, 100, 110], "fs_version": 71, "fs_version_str": 71, "fsaparc": [88, 110], "fsavaerag": 70, "fsaverag": 90, "fslmer": 90, "fsqsphere": [88, 110], "fssl": 89, "fstess": [88, 110], "fstutori": 86, "fswiki": 86, "full": [15, 34, 38, 47, 50, 62, 71, 87, 89, 90, 92, 94, 95, 96, 98, 99, 102, 107, 109, 110, 112], "full_ipv": 47, "full_nbr_label": 47, "full_nbr_mean": 47, "full_pv": 47, "full_seg_mean": 47, "fulli": [23, 42, 83, 96, 99], "func": 50, "function": [14, 15, 18, 20, 23, 24, 25, 29, 30, 31, 33, 41, 42, 47, 50, 54, 56, 59, 61, 62, 65, 66, 70, 71, 74, 75, 81, 85, 89, 94, 99, 100, 105, 110], "fund": [83, 96], "further": [84, 91], "furthermor": [86, 87], "fuse": [23, 34, 42], "fuse_cortex_label": 34, "futur": [33, 34, 46, 47, 50, 59, 86, 88, 109], "future1": 34, "future2": 34, "fz": [104, 107], "g": [34, 47, 50, 54, 61, 69, 70, 73, 75, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 96, 99, 100, 102, 103, 104, 105, 107, 110, 111], "gamma": 68, "gap": 21, "gaussian": [14, 32, 43], "gaussiannois": 43, "gb": [89, 94, 96, 100], "gckeepstorag": 94, "gcpolici": 94, "geforc": 92, "gen": 85, "gender": 84, "gener": [14, 28, 34, 54, 61, 66, 87, 88, 90, 91, 92, 95, 97, 99, 100, 107, 110], "generate_bias_field": 14, "generate_binary_structur": 30, "generate_hdf5": [81, 108, 112], "geometri": 91, "german": [83, 96], "get": [15, 23, 24, 28, 32, 33, 34, 35, 42, 43, 46, 47, 49, 50, 60, 61, 63, 64, 67, 87, 88, 89, 92, 94, 96], "get_adjm": 79, "get_aseg_cereb_mask": 15, "get_attribut": 50, "get_bounding_offset": 16, "get_brain_centroid": 67, "get_cfg": [39, 64], "get_checkpoint": [26, 49], "get_checkpoint_path": [26, 49], "get_color_by_index": 54, "get_common_suffix": 50, "get_config": [27, 51], "get_conformed_vox_img_s": 33, "get_dataload": [17, 36], "get_default_version_info": 61, "get_devic": [39, 64], "get_epoch_lr": 28, "get_image_mean": 67, "get_img": 46, "get_img_metadata": 16, "get_label": 16, "get_labels_from_lut": 34, "get_largest_cc": 34, "get_loss_func": 41, "get_lr": 28, "get_lr_schedul": [28, 53], "get_max_s": [39, 64], "get_model_height": [39, 64], "get_model_width": [39, 64], "get_modelnam": [39, 64], "get_nibabel_img": 16, "get_num_class": [39, 46, 64], "get_num_thread": 60, "get_orig": 16, "get_plan": [39, 64], "get_predict": [46, 66], "get_random_param": 14, "get_region_bg_intersection_mask": 44, "get_seg_centroid": 69, "get_subject_nam": [16, 35, 46], "get_tal_origin_voxel": 67, "get_thick_slic": 34, "get_ventricle_bg_intersection_volum": 44, "get_vox2ra": 69, "getitem_by_index": 54, "getscal": 33, "getsurfcorrespond": 73, "getter": 46, "gihub": 85, "gil": 34, "gist_ncar": 54, "git": [61, 71, 85, 87, 88, 89, 94], "git_branch": [61, 88], "git_hash": 61, "git_process": 61, "git_statu": 61, "github": [14, 85, 87, 89, 90, 93, 94], "githubusercont": 89, "give": [41, 46, 50, 53, 88, 97, 110], "given": [13, 18, 20, 25, 26, 27, 28, 30, 32, 34, 36, 38, 41, 44, 46, 48, 49, 50, 51, 63, 64, 70, 78, 87, 96, 98, 99, 103, 106, 110], "glibcxx": 89, "glob": 100, "global": [23, 29, 42, 47, 87, 88, 90, 94, 98, 110], "global_crop": 47, "global_stat": 47, "global_step": [29, 55], "gm": [78, 83, 90, 105], "gm_binari": 21, "gm_mask": 38, "gn": 43, "gn0": 43, "gn1": 43, "gn2": 43, "gn3": 43, "gn4": 43, "gn_nois": 35, "go": [47, 85, 94], "goal": 90, "good": 84, "goodwil": 97, "googl": 95, "gpu": [26, 49, 83, 87, 88, 90, 92, 96, 99, 100, 102, 103, 106, 107, 111], "gpu_partit": 87, "gracefulli": 84, "gradient": [34, 38, 105], "grai": [21, 34, 86, 91], "grant": 97, "graph": [23, 24, 42, 43], "graphic": [89, 96], "great": 96, "greater": [48, 87, 88, 89], "grei": 34, "grep": 100, "greve": 90, "grid": 30, "grossli": 97, "ground": [29, 34, 38, 56, 105], "group": [14, 30, 47, 56, 87, 89, 90, 94, 96, 100], "grow": 47, "gt": [29, 30, 34], "gt_name": 105, "gt_nocc": 105, "guarante": [67, 111], "guess": 34, "gui": 85, "guid": [47, 85, 87, 89, 98], "guidelin": 85, "gyri": 86, "gz": [66, 87, 88, 91, 92, 94, 99, 100, 102, 103, 107], "h": [15, 41, 42, 43, 47, 85, 87, 88, 102, 103, 104, 105, 106, 107, 109, 110], "h5py": [38, 89], "h5pydataset": 38, "ha": [41, 50, 65, 67, 70, 85, 87, 88, 89, 90, 94, 96, 97, 98, 99, 105, 107, 110], "had": 89, "half": [87, 88], "handi": 92, "handl": [46, 47, 50, 54, 65], "handle_cuda_memory_except": 50, "happen": [85, 100], "harass": 84, "hard": [34, 85, 86], "hardwar": [94, 102, 103, 107, 111], "harm": [84, 86], "harmless": 97, "harvard": [86, 87, 88, 92, 98, 110], "has_attribut": 50, "has_git": 61, "hash": [61, 71, 94], "hausdorff": 30, "have": [14, 20, 30, 34, 50, 56, 65, 66, 68, 78, 84, 85, 86, 87, 88, 89, 90, 91, 92, 94, 96, 97, 99, 100, 102, 103, 105, 107, 110], "hd": [30, 88, 109], "hd50": 30, "hd95": 30, "hdf5": [18, 38, 89, 105, 106], "hdf5_dir": 89, "hdf5_name": 105, "hdf5_set": [105, 106], "head": [88, 89, 90, 92, 96, 102, 103, 107, 109, 110], "header": [13, 21, 33, 34, 47, 54, 66, 72, 73, 75, 111], "header_info": 34, "heavi": 87, "height": [13, 39, 42, 64, 65, 106], "help": [46, 47, 50, 58, 85, 86, 87, 88, 89, 90, 94, 96, 99, 100, 108, 110], "helper": [87, 90], "helpformatt": 47, "hemi": [34, 70, 95, 110], "hemispher": [34, 38, 45, 70, 87, 88, 91, 99, 110], "henschel": [83, 88, 96, 109, 110], "here": [70, 84, 87, 88, 89, 90, 92, 94, 96, 98, 100, 103, 105, 109], "herebi": 97, "herein": 97, "hhmmss": 100, "hidden": 99, "high": [33, 34, 83, 88, 96, 107, 109], "higher": [33, 78, 89], "highest": 33, "highli": [83, 90], "highlight": 90, "highr": [83, 88, 96, 109, 110, 111], "hint": 54, "hippocampu": 96, "hire": [34, 38, 105, 110], "hires_w": 105, "hires_weight": 38, "histori": 85, "hold": [33, 44, 45, 51, 67, 69, 70, 71, 73, 74, 75, 76, 77, 78, 79, 80, 97], "hole": [21, 79], "home": [49, 86, 87, 88, 89, 90, 92, 94, 99, 100, 102, 103, 106, 107, 109, 110], "homebrew": 89, "homer": 98, "homogen": 68, "hook": 39, "hope": 86, "horizont": 14, "host": [49, 89, 94, 98], "hot": [56, 88], "hous": 96, "how": [33, 47, 86, 87, 89, 92, 93, 94, 95, 96, 98], "howev": [33, 86, 87, 97, 100, 107, 110, 111], "hpc": [94, 98], "hpcwork": [87, 100], "hsa_override_gfx_vers": 94, "html": [28, 84, 87, 88, 89, 94, 98, 110], "http": [14, 25, 28, 83, 84, 85, 86, 87, 88, 89, 90, 92, 94, 96, 97, 98, 104, 107, 109, 110, 111], "httperror": 49, "hub": 94, "human": [89, 96], "hyperintens": 14, "hypo_map_label2subseg": 62, "hypo_map_prediction_sagittal2ful": 62, "hypo_map_subseg_2_fsseg": 62, "hypo_maskfil": 66, "hypo_segfil": [66, 107], "hypointens": 34, "hypoth": 83, "hypothalam": [83, 92, 96, 107], "hypothalamu": [66, 83, 86, 88, 91, 96, 107, 109], "hypothalamus_mask": [66, 91, 107], "hypterthread": 87, "hypvinn": [81, 83, 88, 95, 96, 99, 101, 104, 108, 109], "hypvinn_axial_v1": 107, "hypvinn_coronal_v1": 107, "hypvinn_qc_screenshoot": 107, "hypvinn_sagittal_v1": 107, "hypvinn_seg": 107, "hypvinndataset": 63, "i": [14, 15, 20, 21, 25, 26, 28, 29, 30, 33, 34, 41, 44, 46, 47, 48, 49, 50, 53, 54, 56, 58, 59, 61, 62, 64, 65, 66, 67, 69, 70, 73, 75, 76, 78, 79, 80, 81, 83, 84, 86, 87, 88, 89, 91, 92, 94, 95, 96, 97, 98, 99, 100, 102, 103, 104, 105, 106, 107, 109, 110, 111], "i1": 90, "icon": 92, "icv": [87, 88, 110], "id": [15, 19, 33, 34, 38, 44, 47, 50, 54, 66, 69, 70, 71, 73, 77, 78, 79, 87, 88, 89, 90, 92, 94, 98, 100, 102, 103, 105, 107, 109, 110, 111], "idea": [85, 90], "ideal": 99, "ident": [68, 79, 84, 85, 88, 94], "identif": 94, "identifi": [15, 85, 100], "idx": 31, "ignor": [33, 41, 61, 88, 107, 111], "ignore_fs_vers": [88, 110], "ignore_index": 41, "ii": [88, 89, 97, 99, 109], "iii": [89, 97, 99], "imag": [13, 14, 15, 18, 20, 21, 23, 24, 29, 30, 32, 33, 34, 35, 38, 39, 40, 42, 43, 46, 47, 50, 54, 57, 62, 63, 65, 66, 67, 69, 78, 83, 86, 87, 88, 89, 90, 91, 92, 95, 96, 99, 100, 102, 103, 105, 106, 109, 110, 111], "imag_a_00034": [83, 88, 96, 107, 109], "image2": 34, "image_nam": [46, 105], "image_path": 100, "image_shap": 20, "imageri": 84, "images_batch": [31, 57], "img": [15, 20, 31, 32, 33, 34, 35, 38, 62, 69, 78], "img1": 47, "img2": 47, "img_arrai": 34, "img_batch": 29, "img_data": [13, 21, 34, 62], "img_filenam": [34, 39], "img_kei": 15, "img_label": 78, "img_lut": 78, "img_org": 16, "img_path": 13, "img_siz": [33, 47], "img_vol": 34, "imglut": 78, "impact": [88, 102, 103, 107, 110, 111], "implement": [14, 25, 41, 47, 54, 89, 94, 100], "impli": [30, 88, 97], "implicitli": [20, 61], "import": [34, 58, 86, 88, 91, 97, 111], "imposs": 86, "improperli": 76, "improv": [86, 96, 97], "in_cooldown": 28, "in_dir": [58, 102, 103], "inabl": 97, "inaccur": 86, "inaccuraci": [33, 86], "inaparcnam": 79, "inappropri": 84, "incid": 84, "incident": 97, "incl": 91, "includ": [13, 14, 15, 22, 33, 34, 47, 50, 54, 61, 65, 71, 79, 83, 84, 85, 86, 87, 88, 89, 91, 92, 93, 94, 97, 98, 103, 105, 106, 107, 110], "inclus": [84, 97], "incompat": [85, 94, 98, 102], "inconsist": [20, 34, 66], "incorpor": 97, "incortexnam": 79, "increas": [33, 90, 94, 96, 100], "incur": 97, "indemn": 97, "indemnifi": 97, "indent_incr": 47, "independ": [83, 88, 90, 94, 96, 99, 107, 109, 110], "index": [20, 34, 41, 47, 54, 63, 73], "indic": [24, 25, 43, 47, 78, 86, 90, 97, 100], "indirect": 97, "indirectli": 111, "individu": [84, 85, 88, 90, 96, 97, 99, 100, 110], "induc": 90, "infer": [25, 35, 46, 47, 63, 66, 81, 88, 102, 103, 107, 111], "infer_labels_excludeid": 47, "infer_mapping_from_lut": 34, "infer_merged_label": 47, "infin": 48, "inflat": [88, 91, 110], "influenc": 30, "info": [20, 33, 61, 72, 88, 94], "inform": [13, 20, 33, 34, 47, 48, 61, 63, 70, 75, 83, 84, 85, 86, 88, 89, 90, 92, 94, 97, 98, 103, 107, 110], "infring": 97, "inher": 90, "inherit": 86, "init_pr": 39, "initi": [27, 30, 39, 42, 47, 51, 56, 62, 65, 83, 86, 88, 90, 91, 96], "inner": [34, 78], "inp_block": 42, "inplac": [39, 47], "input": [14, 23, 24, 29, 30, 32, 33, 34, 38, 41, 42, 43, 45, 47, 50, 54, 56, 61, 62, 63, 65, 66, 67, 75, 76, 79, 83, 85, 86, 87, 88, 90, 99, 102, 103, 105, 106, 109, 110, 111], "input_dir": 70, "input_norm": 111, "input_seg": 111, "inputdenseblock": [43, 65], "inputx": 41, "insid": [46, 67, 78, 79, 87, 88, 94, 98, 109], "inspect": [86, 87], "inspir": 25, "instal": [61, 87, 88, 90, 92, 94, 95, 96, 98, 99, 104], "install_env": 89, "instanc": [64, 65, 84], "instead": [23, 33, 42, 47, 58, 75, 80, 85, 86, 88, 92, 98, 105, 110], "institut": 97, "instruct": [87, 89, 92], "insult": 84, "insurf": 75, "insurfnam": 79, "int": [13, 15, 16, 20, 25, 26, 28, 29, 30, 33, 34, 38, 39, 41, 44, 45, 46, 47, 48, 49, 50, 54, 55, 56, 57, 60, 61, 62, 63, 64, 65, 66, 67, 69, 71, 78, 79, 80, 88, 110], "int8": 47, "int_ge_zero": 48, "int_gt_zero": 48, "integ": [41, 44, 47, 48, 54, 79, 111], "integr": 86, "intend": [33, 86, 95, 98], "intens": [14, 33, 47, 67, 111], "intention": 97, "interact": 92, "interest": [34, 47, 84, 92], "interfac": [71, 73, 74, 75, 76, 77, 78, 79, 80, 85, 97, 102, 107, 110, 112], "interleav": [99, 110], "intermedi": [86, 87, 88, 100, 102, 103, 110], "intern": [30, 50, 54, 62, 81, 90, 105], "interpol": [20, 33, 34, 40, 42, 43, 65, 106], "interpol1": [42, 65], "interpol2": [42, 65], "interpolation_lay": 81, "interpolation_mod": [40, 42, 65], "interpret": [50, 85, 111], "intersect": [30, 44, 56], "intersection_volum": 44, "intervent": 86, "intracrani": [86, 92], "intricaci": 87, "introduct": [90, 92, 95], "introduction_to_amd_rocm_installation_guide_for_linux": 89, "invalid": [20, 47, 48, 65, 66, 67, 100], "invers": [33, 54, 90], "investig": 84, "invit": 86, "invok": [87, 110], "io": [87, 89, 94, 100], "ioerror": 34, "iornt": 62, "iou_scor": 56, "ipc": 89, "ipv": 47, "irrevoc": 97, "is_bett": 28, "is_biject": 54, "is_checkpoint_epoch": 26, "is_conform": 33, "is_int": 54, "is_lia": 33, "is_resampling_vox2vox": 33, "island": [45, 78], "isol": 85, "isometr": 88, "isotrop": [33, 34, 78, 83, 87, 88, 103, 110], "issu": [84, 85, 86, 89, 90, 93, 97], "item": [47, 50], "iter": [29, 34, 45, 47, 50, 55, 58, 64, 67, 86, 88, 110], "itk": [67, 88, 110], "itk_aseg": 67, "itk_bfcorr_imag": 67, "itk_imag": 67, "itk_mask": 67, "itk_n4_bfcorrect": 67, "its": [13, 14, 46, 54, 59, 67, 79, 84, 87, 89, 94, 97, 98, 102, 103, 110], "itself": [103, 107], "j": [25, 78, 83, 88, 90, 96, 109, 110], "januari": 97, "job": [87, 100], "job_arrai": 100, "jobarrai": [99, 100], "jobarrayid": 100, "joint": 90, "json": [54, 94], "jsoncolorlookupt": 54, "juelich": [104, 107], "just": [20, 33, 70, 76, 85, 87, 88, 89, 90, 92, 98, 110], "j\u00fclich": 107, "k": [14, 83, 88, 92, 96, 109, 110], "kdtree": 73, "keep": [14, 33, 34, 54, 55, 85, 111], "keep_label": 54, "keep_strictly_posit": 14, "keepbyt": 94, "keepdur": 94, "kei": [15, 47, 54, 58, 61, 66, 88, 94, 110], "kernel": [47, 89, 94, 106], "kernel_c": [24, 43], "kernel_h": [24, 43, 106], "kernel_w": [24, 43, 106], "keypair": 94, "keyword": [34, 47, 50, 80], "kfd": [89, 94], "kill": 100, "kind": 97, "know": 90, "kpend": 100, "kt": 54, "kuegler": [25, 54, 83, 88, 96, 99, 100, 109, 110], "kueglrun": 100, "kuegpend": 100, "kuegrun": 100, "kwarg": [28, 34, 47, 50, 58, 59, 80], "k\u00fcgler": [99, 100, 107, 111], "l": [83, 85, 88, 96, 109, 110], "lab": 47, "label": [13, 14, 15, 20, 21, 29, 30, 31, 32, 34, 35, 38, 41, 44, 45, 47, 54, 55, 57, 62, 67, 69, 70, 73, 77, 78, 79, 83, 85, 86, 91, 96, 103, 105, 110, 111], "label_batch": 29, "label_extract": 34, "label_id": [69, 77], "label_list": 14, "label_map": 15, "label_nam": 70, "label_typ": [15, 20], "label_vol": 34, "labeldir": 70, "labelnam": [34, 47, 73, 105], "labelname2id": 54, "labelname2index": 54, "labels_batch": [31, 57], "labels_dst": 77, "labels_list": 14, "labels_mov": 77, "labels_new": 79, "labels_sag": [34, 38], "lambda": [30, 56], "landau": 94, "languag": 84, "laplac": 47, "larg": [47, 83, 91, 94, 96, 103, 111], "larger": [70, 87, 89], "largest": [16, 34, 78, 89, 103, 111], "last": [20, 24, 26, 31, 43, 61, 92, 102, 103, 107, 111], "last_epoch": 28, "later": [34, 38, 44, 86, 89, 92, 109], "latest": [57, 85, 87, 89, 92, 94, 98, 110], "latter": [94, 100], "law": 97, "lawsuit": 97, "layer": [23, 24, 34, 42, 43, 63, 65, 106], "layout": 33, "lbl_data": 15, "lbl_kei": 15, "lbl_path": 13, "lbl_type": 15, "lead": [20, 48, 58, 90], "leadership": 84, "learn": [14, 25, 28, 29, 53, 55, 63, 74, 83, 88, 96, 99, 102, 106, 109, 110], "learnabl": 43, "least": [68, 88, 89, 96, 97], "leav": 61, "left": [15, 21, 34, 38, 44, 47, 53, 69, 87, 91, 99, 103, 105], "legaci": 47, "legacy_freesurf": [47, 111], "legal": 97, "len": 14, "length": [14, 30], "less": [20, 92, 96], "let": 96, "level": [48, 66, 67, 84, 94], "lh": [34, 70, 73, 86, 91], "lhcerebralwhitematt": 111, "lhcortex": 111, "lhsurfacehol": 111, "lia": [15, 33, 87, 110], "liabil": 97, "liabl": [96, 97], "lib": 94, "librari": [85, 103, 106], "libstdc": 89, "licens": [86, 87, 88, 89, 90, 92, 94, 95, 96, 98, 99, 100, 110], "licensor": 97, "like": [34, 47, 58, 61, 67, 71, 89, 94, 99, 100, 103], "likelihood": 41, "limit": [47, 94, 97, 99, 100, 103], "line": [25, 33, 44, 45, 47, 61, 66, 67, 69, 70, 71, 73, 74, 75, 76, 77, 78, 79, 80, 85, 87, 89, 99, 100, 103, 106, 110], "linear": [28, 33, 34, 72, 90], "linearsegmentedcolormap": [31, 57], "link": [54, 87, 91, 92, 96, 97], "linux": [85, 92, 94, 95], "list": [14, 26, 29, 31, 34, 35, 38, 46, 47, 49, 50, 54, 57, 58, 61, 69, 70, 71, 73, 78, 79, 84, 86, 89, 94, 95, 97, 98, 100, 103, 105, 106, 108, 109, 110, 111], "liter": [16, 47, 58], "litig": 97, "littl": [88, 110], "lme": 90, "load": [13, 16, 17, 18, 19, 22, 26, 27, 31, 33, 34, 35, 36, 38, 39, 49, 51, 57, 58, 63, 64, 66, 73, 94, 99, 102, 103, 104, 105, 106], "load_and_conform_imag": 34, "load_aux_data": [16, 18, 19], "load_checkpoint": [39, 64], "load_checkpoint_config": 49, "load_checkpoint_config_default": 49, "load_classwise_weight": 31, "load_config": 81, "load_data": 81, "load_from_checkpoint": [26, 49], "load_imag": 34, "load_maybe_conform": 34, "load_subject": 19, "load_test_subject": 19, "load_volum": 66, "loaded_epoch": [26, 49], "loader": [16, 19, 39, 57, 81], "loc": 75, "local": [34, 47, 85, 87, 88, 92, 94, 98, 110], "local_rank": [30, 56], "locat": [47, 61, 87, 88, 90, 94, 102, 103, 109, 110], "locate_mask_bbox": 16, "locating_unknown": 21, "log": [29, 33, 34, 41, 55, 80, 81, 85, 88, 91, 100, 102, 103, 106, 107, 110], "log_dir": [26, 49, 106], "log_epoch": [29, 55], "log_file_path": 52, "log_it": [29, 55], "log_lr": 29, "log_nam": [102, 103, 107], "logfil": [52, 91, 99, 103], "logger": [33, 34], "logit": [23, 24, 42, 43, 65], "long": [41, 88, 90, 108, 110], "long_fastsurf": [88, 90, 108], "long_prepare_templ": [88, 90], "longer": [89, 92, 94], "longitudin": [14, 88, 95, 109, 110], "longitudion": 90, "longtensor": 41, "look": [20, 34, 62, 78, 85, 92, 99, 100], "lookup": [34, 47, 103, 105], "loop": 99, "loss": [23, 29, 42, 55, 81, 97], "loss_c": 55, "loss_dic": 55, "loss_dict": 29, "loss_tot": 55, "lot": 85, "low": 33, "lower": [24, 43], "lr": [28, 29, 53, 55], "lr_func_cosin": 28, "lr_restart": 28, "lr_schedul": [81, 106], "lta": [20, 81, 86, 107], "ltadict": 20, "lut": [34, 38, 39, 46, 47, 92, 103, 105, 111], "lut_fil": 34, "m": [78, 79, 83, 87, 88, 89, 96, 99, 107, 109, 110], "m1": [89, 94], "m1_inp_block": 65, "m2": 89, "m2_inp_block": 65, "mac": [88, 89, 94], "machin": [92, 94, 100], "maco": [85, 95], "made": [97, 100], "mai": [20, 61, 84, 86, 87, 88, 89, 91, 94, 96, 97, 99, 100, 102, 103, 107, 110], "mail": [84, 97], "main": [13, 25, 42, 47, 50, 61, 66, 70, 79, 83, 89, 94, 103, 106, 110], "main_segfil": [50, 88], "maintain": [84, 85], "major": 85, "make": [69, 75, 84, 85, 87, 89, 90, 94, 96, 97, 98, 110], "make_argu": 47, "make_classmapp": 54, "make_pars": [33, 46, 61, 76], "make_subjects_dir": 50, "malfunct": 97, "mame": 54, "mammilar": 83, "man": 86, "manag": [22, 47, 85, 87, 89, 97], "mandatori": 88, "manedit": [86, 88, 110], "mani": [47, 85, 87, 88, 91, 94], "manifold": 78, "manner": 99, "manual": [87, 88, 94, 95, 98, 99], "manual_cereb": 21, "map": [15, 20, 23, 24, 29, 31, 33, 34, 38, 39, 43, 47, 50, 54, 57, 58, 62, 70, 73, 74, 77, 83, 86, 87, 88, 90, 91, 92, 94, 96, 98, 105, 110], "map_aparc_aseg2label": 34, "map_imag": 33, "map_label2aparc_aseg": 34, "map_label2subseg": 20, "map_logit": 54, "map_multiple_label": 70, "map_prediction_sagittal2ful": [15, 34], "map_prob": 54, "map_sag2label": 15, "map_siz": 20, "map_surf_label": 81, "mapped_aseg": 34, "mapped_subseg": [20, 62], "mapper": 81, "mapsurflabel": 73, "march": [75, 88, 110], "mark": [85, 97], "martin": [84, 107], "mask": [15, 16, 21, 32, 34, 38, 44, 45, 47, 58, 66, 67, 70, 79, 86, 87, 91, 92, 103, 105, 107, 110, 111], "mask_fil": 110, "mask_nam": [88, 110], "maskvol": 111, "mass": 90, "massiv": 94, "match": [33, 34, 38, 63, 103, 105], "materi": 94, "matlab": 90, "matplotlib": [31, 57], "matric": [56, 88, 110], "matrix": [13, 29, 31, 33, 55, 56, 57, 67, 68, 69, 77, 78, 79, 86], "matter": [14, 21, 34, 45, 61, 67, 70, 91, 95], "max": [24, 33, 38, 39, 43, 47, 54, 87, 88, 99, 105, 109, 110], "max0": 16, "max1": 16, "max_edge_weight": [15, 34], "max_epoch": 28, "max_help_posit": 47, "max_hires_weight": 34, "max_it": 28, "max_label": [47, 54], "max_siz": 33, "max_unpool2d": 89, "max_w": 105, "max_weight": [34, 38], "maxim": [33, 34], "maximum": [15, 30, 39, 47, 50, 54, 64, 67, 111], "maximum_intens": 47, "maxout": [23, 24, 42, 43], "maxpool": [24, 43], "mayb": [46, 85], "md5sum": 61, "mean": [14, 29, 30, 32, 41, 47, 56, 62, 67, 87, 88, 97, 103, 110, 111], "mean_filt": 34, "meantim": 85, "measur": [47, 96], "measure_onli": 111, "measurefil": [47, 111], "mechan": 97, "media": [84, 97], "median": [14, 15, 31, 34, 38, 105], "medium": 97, "meet": 97, "mem": 100, "mem_seg": 100, "mem_surf": 100, "member": [84, 85], "memori": [20, 50, 88, 89, 94, 96, 99, 100, 102, 103, 107], "mention": 111, "merchant": 97, "mere": 97, "merg": [47, 54, 85, 88, 96], "merge_label": 47, "merge_labels_start": 47, "merged_label": [47, 111], "merit": 85, "mesh": 79, "messag": [25, 33, 34, 39, 47, 50, 54, 59, 61, 66, 102, 103, 107], "messagebuff": 59, "met": 94, "meta": 47, "meter": 81, "method": [14, 16, 18, 19, 20, 22, 23, 24, 25, 28, 29, 30, 32, 35, 38, 39, 40, 41, 42, 43, 46, 47, 49, 50, 54, 55, 56, 58, 59, 61, 63, 64, 65, 83, 85, 88, 96, 106, 107, 109, 110], "methodolog": 90, "metric": [26, 28, 29, 49, 81, 103, 111], "metrics_per_class": 29, "mgh": [21, 86, 87, 88, 92, 98, 110], "mghimag": [33, 34], "mgz": [34, 58, 69, 75, 86, 87, 88, 89, 90, 91, 92, 96, 98, 100, 102, 103, 105, 107, 110, 111], "mi": [84, 85, 87, 89, 90], "mid": [69, 90], "mid_slic": 69, "middl": [23, 34, 42], "might": [92, 94, 98, 99], "millimet": 83, "mimic": 83, "min": [33, 34, 46, 47, 48, 88, 96, 103, 110], "min0": 16, "min1": 16, "min_dim": 33, "min_memori": 50, "mind": 85, "miniconda": 89, "miniconda3": 89, "minim": [33, 34, 58, 88], "minimum": [33, 34, 47, 50, 89, 103], "minimum_intens": 47, "ministri": [83, 96], "minor": [85, 86], "minut": [83, 87, 92, 96, 100], "misc": [81, 112], "miss": [21, 47, 56, 61, 66, 70, 72, 86, 89, 100], "mix": [90, 111], "mixing_coeff": [47, 111], "mkdir": 92, "mm": [30, 33, 78, 92], "mmb": [83, 88, 96, 109], "mod_weight": 65, "modal": [63, 64, 65, 66, 107], "modalitydict": [64, 66], "modalitymod": [64, 66], "mode": [17, 29, 33, 36, 42, 47, 55, 63, 64, 65, 66, 79, 88, 89, 94, 99, 110], "mode_filt": 79, "model": [22, 26, 30, 39, 46, 49, 56, 63, 64, 66, 81, 90, 91, 92, 104, 112], "model_nam": [39, 64, 106], "model_parallel": 39, "modern": 89, "modif": [97, 100], "modifi": [34, 74, 86, 90, 97, 111], "modul": [26, 39, 49, 64, 66, 80, 81, 86, 89, 92, 95, 103, 106, 107], "moment": 94, "momentum": 106, "monei": 90, "moniqu": 107, "more": [30, 33, 48, 50, 68, 86, 87, 88, 90, 92, 94, 97, 98, 99, 107, 111], "morphologi": 30, "most": [30, 34, 47, 56, 85, 86, 87, 88, 89, 90, 94, 96, 100, 102, 107, 110], "motion": 96, "mount": [87, 88, 94, 99, 110], "mousa": [83, 88, 96, 107, 109], "mov": 69, "move": [15, 39, 62, 73, 77, 87, 100], "mp": [88, 89, 94], "mr": [47, 88, 96, 110, 111], "mri": [13, 14, 34, 35, 58, 63, 83, 86, 87, 88, 89, 90, 91, 92, 94, 96, 98, 100, 102, 103, 105, 107, 109, 110, 111], "mri_convert": 33, "mri_coreg": [88, 107], "mri_mc": [88, 110], "mri_robust_regist": [88, 107], "mri_robust_templ": 90, "mri_segstat": [47, 111], "mri_tessel": [88, 110], "mri_vol2vol": 107, "mri_volum": 103, "mris_preproc": 90, "mris_regist": 68, "much": [47, 85, 89, 94, 96], "mul": 47, "multi": [30, 47, 56, 88, 102, 103, 106, 107, 111], "multipl": [34, 47, 70, 71, 89, 90, 94, 95, 99, 103], "multires_coron": 105, "multiscaledataset": 35, "multiscaledatasetv": 35, "multiscaleorigdatathickslic": 35, "must": [14, 20, 30, 33, 47, 48, 88, 94, 97, 98, 100, 103, 110], "must_keep_id": 47, "mutablesequ": [26, 49], "my": [85, 92], "my_fastsurf": [89, 94], "my_fastsurfeer_analysi": 110, "my_fastsurfer_analysi": [86, 87, 89, 90, 94, 98, 110], "my_fs_license_dir": [87, 89, 90, 94, 98, 110], "my_mri_data": [87, 89, 90, 94, 98, 110], "my_recon_surf_output": 110, "my_segmentation_data": 110, "my_singlarity_imag": 98, "myaccount": 94, "myimag": 98, "n": [20, 34, 41, 42, 43, 62, 67, 78, 79, 87, 99, 100, 107, 109], "n4_bias_correct": 81, "n_epoch": 28, "n_iter": 28, "na": [83, 88, 96, 109], "name": [13, 15, 26, 31, 34, 35, 38, 39, 47, 49, 50, 54, 57, 58, 61, 64, 66, 70, 71, 73, 75, 76, 78, 79, 86, 87, 88, 90, 94, 96, 97, 98, 100, 110], "name1": 47, "name2": 47, "namespac": [25, 47, 51, 67, 71, 73, 74, 75, 76, 77, 78, 79, 80], "nation": 84, "nativ": [54, 83, 86, 88, 94, 95, 96, 99, 104], "native_t1_fil": 50, "nbr": 47, "nbr_mean": 47, "nbr_mixing_coeff": 47, "nclass": 56, "ndarrai": [13, 14, 15, 20, 31, 32, 33, 34, 35, 38, 39, 44, 45, 46, 47, 54, 56, 57, 62, 63, 64, 66, 67, 68, 69, 70, 73, 77, 78, 79], "ndimag": 30, "nearest": [33, 34, 40, 65], "necessari": [47, 84, 85, 86, 87, 89, 98, 100], "necessarili": 97, "need": [15, 20, 26, 33, 34, 70, 78, 83, 85, 86, 87, 88, 89, 90, 91, 92, 94, 98, 100, 102, 103, 106, 107, 109, 110], "neg": [20, 41, 48, 56, 79], "neglig": 97, "neighbor": 47, "neighborhood": 47, "neighbourhood": 30, "neither": [20, 48], "nesterov": 106, "net": 94, "network": [15, 16, 26, 28, 34, 35, 39, 46, 49, 56, 62, 63, 81, 83, 86, 88, 89, 103, 104, 106, 110], "neural": [39, 86, 88, 89, 104], "neuroimag": [22, 25, 83, 88, 90, 96, 109, 110], "neurosci": [83, 88, 96, 107, 109], "never": [33, 47, 85], "new": [33, 54, 62, 79, 85, 86, 89, 90, 94], "new_iornt": 62, "newer": 89, "newest": 94, "newlin": 47, "next": [50, 85, 88, 89, 90], "next_messag": 59, "ni": 85, "nib": [33, 34, 46, 92], "nibabel": [13, 34, 47, 62, 78, 79, 111], "niclei": 90, "nifti": [13, 33, 34, 90, 92], "nifti1head": 13, "nifti1imag": [33, 62], "nifti2head": 13, "nifti2imag": 33, "niftynet": 14, "nii": [66, 87, 88, 91, 92, 94, 99, 100, 102, 103, 107], "nipi": 111, "nj": [88, 109], "nll_loss": 41, "nmr": [86, 87, 88, 92, 98, 110], "nn": [26, 39, 49, 64, 65], "no_asegdkt": [83, 88], "no_bias_field": 83, "no_biasfield": [83, 87, 88, 92], "no_cereb": [83, 86, 87, 88, 91, 92, 100], "no_fs_t1": [88, 110], "no_grad": 105, "no_hypoth": [83, 86, 87, 88, 91, 92], "no_surfreg": [88, 110], "node": [26, 31, 36, 39, 41, 42, 46, 49, 51, 53, 64, 65, 66, 87, 100], "nois": [32, 43], "nomenclatur": 91, "non": [20, 29, 47, 59, 78, 79, 88, 89, 97], "none": [14, 16, 19, 20, 26, 28, 29, 30, 31, 33, 34, 35, 39, 41, 42, 46, 47, 48, 49, 50, 53, 54, 55, 56, 58, 59, 61, 63, 64, 65, 66, 67, 69, 70, 73, 76, 77, 78, 79, 88, 102, 105, 106, 107, 111], "nor": 20, "norm": [24, 43, 47, 67, 88, 102, 110, 111], "norm_nam": [47, 88, 102, 111], "norm_unit": [47, 111], "normal": [23, 42, 43, 47, 65, 67, 78, 88, 97, 105, 110], "normalize_img": 67, "normalize_weight": 65, "normalize_wm_aseg": 67, "normalize_wm_mask_bal": 67, "normalized_imag": 67, "normfil": [47, 111], "normmax": 47, "normmin": 47, "not_empti": 47, "note": [20, 28, 30, 33, 44, 58, 61, 74, 83, 86, 87, 88, 89, 90, 91, 94, 98, 99, 100, 102, 103, 107, 110, 111], "noth": 97, "notic": [86, 94, 97], "notimplementederror": 41, "notwithstand": 97, "nov": [99, 100], "novel": [88, 110], "novot": 79, "now": [89, 94, 96], "np": [15, 20, 29, 31, 32, 33, 34, 35, 38, 44, 45, 46, 47, 56, 62, 63, 67, 73, 78, 79], "npt": [34, 35, 38, 39, 45, 47, 57, 62, 63, 64, 66, 67, 68, 69, 70, 72, 73, 74, 77, 79], "nt": 47, "nu": [88, 110], "null": 100, "num_cases_per_task": 100, "num_channel": [24, 43, 65, 106], "num_class": [24, 30, 34, 43, 56, 65, 106], "num_classes_ful": 34, "num_cpus_per_case_surf": 100, "num_cpus_per_task": 100, "num_epoch": 106, "num_filt": [24, 43, 106], "num_gpu": [26, 49, 106], "num_seg_process": 99, "num_seg_thread": 99, "num_surf_process": 99, "num_surf_thread": 99, "number": [14, 15, 20, 23, 26, 28, 29, 30, 31, 32, 33, 34, 38, 39, 42, 45, 46, 47, 48, 49, 50, 56, 57, 60, 61, 63, 64, 66, 67, 70, 71, 73, 78, 79, 87, 88, 89, 90, 91, 98, 99, 100, 102, 103, 105, 106, 107, 109, 110, 111], "number_of_voxel": 47, "number_of_within_robustness_threshold": 47, "numer": 47, "numit": 67, "numpi": [14, 20, 34, 44, 45, 47, 48, 54, 73, 111], "nv": [87, 90, 92, 98, 99], "nvidia": [88, 89, 94, 96, 102, 103, 107, 111], "nvoxel": 47, "nx3": 73, "o": [26, 39, 49, 66, 70, 85, 89, 92, 94, 110, 111], "ob": 38, "object": [28, 30, 31, 33, 34, 39, 41, 42, 44, 45, 46, 47, 50, 51, 54, 57, 58, 59, 61, 66, 67, 69, 70, 71, 73, 74, 75, 76, 77, 78, 79, 80, 97], "oblig": [84, 97], "obtain": [44, 47, 86, 88, 107, 110], "obviou": 85, "occur": [33, 78], "occurr": 79, "off": [47, 88, 91, 92, 102, 103, 107, 111], "offens": 84, "offer": 97, "offici": [84, 89, 95], "offlin": 84, "offset": [16, 20, 33], "oflabel": 105, "often": 86, "old": 76, "older": [85, 89], "omgwtfssl": 94, "omit": [87, 94], "onc": [85, 87, 89, 94], "one": [23, 30, 33, 34, 42, 47, 48, 54, 56, 70, 79, 85, 86, 87, 88, 89, 90, 92, 94, 97, 99, 100, 103, 110], "one_hot": 30, "ones": [34, 78, 87, 88, 94, 96, 110], "onli": [14, 23, 33, 34, 38, 39, 42, 47, 63, 70, 78, 83, 85, 86, 87, 88, 92, 94, 96, 97, 98, 100, 102, 103, 105, 107, 109, 110, 111], "onlin": [61, 84], "onto": 85, "op": [24, 30, 43, 47, 56], "opac": 92, "open": [84, 85, 86, 89, 96], "openmp": [88, 110], "oper": [22, 24, 33, 43, 45, 47, 66, 78, 86, 89, 100, 102, 103, 107], "oppos": [56, 90], "opt": [89, 94, 102, 106], "optic": [34, 83], "optim": [26, 28, 49, 53, 54, 87, 92, 96, 99, 100, 112], "optimizing_method": 106, "option": [14, 19, 20, 26, 29, 30, 31, 32, 33, 34, 39, 41, 42, 44, 45, 46, 47, 49, 50, 54, 56, 58, 59, 61, 62, 64, 65, 66, 67, 69, 70, 71, 73, 74, 75, 76, 77, 78, 79, 80, 83, 86, 87, 89, 94, 95, 96, 99, 100, 109, 112], "option_pars": 66, "optional_path": 66, "options_pars": [33, 44, 45, 67, 69, 70, 71, 73, 75, 77, 78, 79], "orchestr": [87, 100], "order": [30, 33, 34, 39, 47, 58, 61, 70, 86, 87, 89, 92, 94, 102, 103, 107], "org": [25, 28, 83, 84, 88, 90, 96, 97, 104, 107, 109, 110, 111], "orient": [15, 33, 34, 62, 76, 84, 87, 88, 110], "orig": [34, 46, 50, 58, 66, 86, 88, 89, 91, 92, 98, 100, 102, 103, 105, 107, 110], "orig_data": [34, 35, 39, 46, 63], "orig_nam": [38, 50, 58, 66, 102, 103, 107], "orig_nu": [86, 87, 88, 91, 107, 110], "orig_zoom": [35, 39, 63, 64, 66], "origin": [24, 38, 39, 43, 46, 47, 54, 63, 64, 66, 67, 74, 85, 86, 91, 97, 102, 103, 105, 111], "ornt": 62, "other": [21, 33, 45, 47, 54, 84, 85, 86, 87, 89, 90, 91, 92, 94, 95, 97, 98, 99, 100, 111], "other_mapp": 54, "otherfold": 100, "otherwis": [33, 47, 64, 66, 84, 97, 104, 110, 111], "our": [85, 87, 89, 90, 94, 95, 96, 98, 105, 110], "out": [20, 24, 39, 42, 43, 47, 50, 54, 59, 85, 96, 97, 103, 110], "out_affin": 33, "out_annot": 70, "out_block": [24, 43], "out_dir": [58, 66, 70, 102, 103, 107], "out_encod": [24, 43], "out_label_nam": 73, "out_r": [39, 64], "out_scal": [39, 64, 66], "out_shap": 33, "out_str": 59, "out_tensor_shap": [42, 65], "outannot": 70, "outaparc": 78, "outaparcnam": 79, "outblock": [24, 43], "outer": 34, "outlier": 30, "outp_block": [42, 65], "outpeform": 90, "output": [24, 30, 32, 34, 39, 41, 42, 43, 46, 47, 54, 56, 57, 61, 64, 65, 66, 70, 73, 75, 76, 78, 79, 80, 83, 85, 86, 87, 88, 89, 90, 92, 94, 95, 98, 99, 100, 102, 103, 109, 110, 111], "output_dir": 107, "output_s": 32, "output_seg_stat": 111, "output_transform": [30, 56], "outputdenseblock": [43, 65], "outputdir": 87, "outsid": [79, 86], "outstand": 97, "outsurf": 75, "over": [50, 56, 61, 64, 86, 87, 90, 99], "overal": [38, 105], "overdetermin": 68, "overestim": 86, "overlai": 91, "overrid": 106, "overview": [88, 95], "overwrit": [54, 70, 76, 86, 87, 94, 98], "overwritten": 111, "overwrot": [88, 102, 103, 107], "own": [14, 79, 85, 86, 89, 92, 94, 95, 97, 100, 104], "owner": 97, "ownership": 97, "p": [83, 88, 89, 96, 109], "p_dst": 68, "p_mov": 68, "packag": [61, 85, 88, 90, 94, 98, 109], "packet": 89, "pad": [20, 32, 35, 47, 66], "pad_siz": 32, "pad_size_imag": 32, "pad_size_mask": 32, "pad_slic": 47, "pad_typ": 32, "padded_s": [42, 65], "page": [89, 92, 94], "paint": 74, "paint_cc_into_pr": 81, "paint_in_cc": 74, "pair": [47, 50, 54, 68, 86], "palett": 54, "panda": [34, 47, 54, 111], "paper": [90, 107], "parallel": [34, 39, 47, 50, 85, 88, 90, 94, 95, 96, 100, 108, 109, 110], "parallel_seg": [99, 109], "parallel_surf": [90, 99, 109, 110], "param": [19, 20, 23, 24, 31, 38, 42, 43, 65], "paramet": [13, 14, 15, 19, 20, 21, 24, 25, 26, 28, 29, 30, 31, 33, 34, 35, 36, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 61, 62, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 87, 94, 99, 100, 111], "parcel": [34, 77, 78, 83, 91, 110], "parecl": 77, "parent": [61, 94], "pars": [25, 47, 61, 66, 71, 100], "parse_arg": [47, 58], "parse_build_fil": 61, "parse_fil": 47, "parse_vers": 71, "parser": [25, 33, 44, 45, 46, 47, 58, 61, 66, 67, 69, 70], "parser_default": 81, "part": [47, 83, 87, 88, 97, 100, 102, 110], "parti": 97, "partial": [14, 47, 83, 88, 91, 92, 96, 111], "partici": 90, "particip": [84, 90], "particular": [86, 91, 97], "partit": [87, 100], "partition_seg": 100, "partition_surf": 100, "pass": [30, 44, 47, 50, 54, 61, 63, 70, 73, 83, 87, 88, 89, 90, 91, 92, 98, 99, 100, 102, 103, 107, 109, 110, 111], "pat_is_bord": 47, "pat_is_nbr": 47, "pat_label_count": 47, "pat_label_sum": 47, "patch": [47, 111], "patch_corn": 47, "patch_filt": 47, "patch_neighbor": 47, "patch_siz": [13, 16, 47, 111], "patent": 97, "path": [13, 14, 26, 31, 34, 38, 46, 47, 49, 50, 52, 57, 58, 61, 64, 66, 69, 70, 73, 75, 76, 83, 86, 87, 88, 89, 90, 94, 98, 99, 100, 102, 103, 104, 105, 106, 107, 109, 110, 111], "path_hdf5_train": 106, "path_hdf5_val": 106, "path_to": 110, "path_to_t1": 87, "pathlik": [26, 39, 49], "patient": 96, "pattern": [18, 28, 38, 90, 100, 103, 105, 107], "paulcz": 94, "paulczar": 94, "pd": [34, 38, 47], "pdf": 57, "pem": 94, "peng": 107, "peopl": 85, "per": [23, 33, 42, 47, 56, 87, 88, 91, 99, 100, 111], "per_class": 30, "percent": 97, "percentil": [30, 47], "perform": [20, 28, 34, 39, 40, 47, 50, 54, 62, 65, 67, 83, 85, 86, 87, 88, 89, 90, 94, 96, 97, 99, 100, 107], "perman": 84, "permiss": [84, 96, 97], "permit": 90, "permut": 39, "permute_ord": 39, "perpetu": 97, "person": [84, 90], "pertain": 97, "phase": 28, "physic": 84, "pial": [91, 95], "pick": 98, "pip": [61, 88, 89, 94, 98], "pip3": 89, "pipe": [59, 99], "pipelin": [25, 46, 50, 83, 89, 90, 94, 95, 96, 98, 100, 101, 108, 109], "pipeline_conform_and_save_orig": 46, "pipeline_s": 50, "pixel": [20, 34], "pkl": [102, 103, 104, 107], "place": [87, 94, 97, 98], "placement": 95, "plan": 88, "plane": [15, 16, 38, 39, 46, 49, 58, 64, 66, 105, 106], "platform": [71, 85, 87, 94], "pleas": [81, 83, 85, 88, 89, 93, 96, 107, 109, 110, 111], "pledg": 95, "plexu": 44, "plot": [31, 34, 38, 57, 92], "plot_confusion_matrix": [31, 57], "plot_predict": [31, 57], "plt": [31, 57], "plt_titl": [31, 57], "plu": [47, 100], "plugin": [85, 94], "png": 107, "po": [32, 47], "point": [68, 81, 83, 85, 86, 87, 88, 89, 90, 94, 98, 109, 110], "pointer": 61, "polici": [28, 84, 95], "polit": 84, "pon": 86, "pool": [24, 34, 43, 46, 50, 59, 106, 109], "popen": [59, 61, 80], "popul": [96, 110], "posit": [14, 32, 33, 40, 42, 45, 47, 48, 56, 65, 84, 86], "posixpath": 49, "possibl": [54, 85, 89, 93, 94, 95, 97, 105, 107, 109, 111], "possibli": 85, "post": [39, 84], "post_prediction_mapping_hook": 39, "potenti": [50, 85, 90, 94, 98], "power": [87, 90, 97, 99], "powershel": 89, "ppa": 89, "practic": [95, 110], "pre": [38, 89, 92, 94, 105, 107], "prebuild": 94, "preced": 34, "precis": 56, "precision_recal": 56, "pred": [29, 30, 55, 74], "pred_batch": 29, "pred_cl": 56, "pred_class": 66, "pred_nam": [58, 102, 103, 107, 111], "pred_prob": [39, 64], "predict": [15, 22, 23, 29, 30, 31, 34, 39, 42, 43, 46, 54, 56, 57, 62, 64, 66, 88, 103, 105, 106, 107, 110], "prediction_sag": [15, 34, 62], "prediction_visu": 29, "prefer": [61, 85, 89, 90, 91, 92, 94, 97, 98], "prefer_cach": 61, "prefix": [34, 58, 89], "prelu": [24, 43], "prepar": [16, 66, 87, 88, 90, 97], "prepare_checkpoint": 66, "prepend": [99, 110], "preproc_imag": 47, "preprocess": 47, "present": [34, 38, 91], "presurf": 86, "pretess": 75, "pretess127": 75, "prev": [24, 43], "previou": [24, 39, 43, 85, 90, 99, 100], "primari": [47, 86, 91, 103], "primarili": 86, "primary_slic": 16, "print": [31, 33, 50, 58, 61, 70, 88, 99, 100, 109, 110], "print_build_fil": 61, "prior": [14, 86], "prior_model_path": [26, 49], "privat": 84, "pro": [89, 94], "probabl": [39, 64, 66], "problem": [85, 89], "procedur": [85, 92], "process": [16, 19, 22, 24, 30, 34, 35, 38, 43, 46, 50, 56, 60, 61, 63, 64, 66, 85, 88, 89, 91, 92, 94, 95, 96, 100, 102, 103, 105, 109, 110, 111], "process_funct": [30, 56], "produc": [79, 86, 87, 89, 92, 96, 110], "product": 97, "profession": 84, "prog": 47, "program": [88, 92, 102, 103, 107, 110], "progress": [29, 99], "project": [61, 83, 84, 85, 88, 94, 96, 110], "project_fil": 61, "project_root": 61, "projmm": 78, "promin": 97, "propag": [65, 86], "properli": [75, 107], "properti": [16, 40, 46, 48, 50, 54, 99], "protocol": 96, "proven": 95, "provid": [14, 29, 34, 48, 50, 54, 59, 65, 66, 83, 85, 86, 87, 88, 89, 90, 94, 96, 97, 106, 110], "pth": 64, "pub": 92, "public": [83, 84, 88, 96, 109, 110], "publicli": 97, "publish": [84, 98], "pull": [85, 87, 89, 95, 110], "purpos": [96, 97], "push": [85, 94], "put": [32, 99, 105], "pv": [47, 111], "pv_calc": 47, "pv_calc_patch": 47, "pv_guid": 47, "pv_stat": 47, "pvfile": [47, 111], "pvmeasur": 47, "pvstat": 47, "pwd": [89, 92, 100], "py": [46, 88, 89, 94, 98, 101, 108, 109, 110, 112], "py38_4": 89, "pydata": 111, "pypackag": 61, "pyplot": 31, "pypopen": 59, "pyproject": [61, 94], "python": [33, 54, 61, 88, 92, 94, 98, 103, 106, 107, 109, 110, 111], "python3": [88, 89, 103, 106, 109, 110], "python_cmd": [88, 109, 110], "pythonpath": [89, 94], "pytorch": [17, 28, 36, 50], "pytorch_enable_mps_fallback": 89, "qatool": 92, "qc": [66, 88, 89, 103, 107], "qc_log": 103, "qc_snap": [88, 107], "qc_snapshot": [66, 88, 107], "qform": 33, "qo": [89, 94], "qsphere": [88, 110], "quadrat": [33, 34], "quadro": 92, "qualiti": [86, 92, 96, 107, 110], "quanti": 96, "quantifi": 90, "question": [84, 108], "queue": 99, "quick": [93, 94, 95], "quick_qc": 81, "quickli": 94, "quit": 92, "quot": [48, 100], "r": [34, 54, 68, 73, 77, 85, 89, 90, 105], "ra": [15, 33, 34, 69, 73], "race": 84, "radeon": [89, 94], "radiu": [21, 67, 73, 78], "rais": [20, 34, 41, 47, 48, 49, 50, 53, 54, 58, 65, 66, 67, 68, 70, 72, 73], "ram": 89, "ran": [47, 99, 110], "random": [14, 32, 106], "randomaffin": 14, "randombiasfield": 14, "randomflip": 14, "randomlabelstoimag": 14, "randomli": 32, "rang": [33, 47, 62, 67], "rank": 30, "rare": 86, "ras2ra": [33, 69], "rate": [28, 29, 53, 55, 106], "raw": [54, 89, 99, 100], "re": [33, 34, 46, 47, 83, 85, 86], "reachabl": 49, "read": [20, 34, 47, 59, 61, 67, 70, 71, 78, 79, 85, 88, 111], "read_and_close_vers": 61, "read_annot": 78, "read_classes_from_lut": 34, "read_colort": [70, 71], "read_geometri": 78, "read_lta": 20, "read_multiple_label": 70, "read_talairach_xfm": 67, "read_version_from_project_fil": 61, "readabl": 97, "readi": 89, "readm": [83, 89, 94, 96], "real": 30, "realist": 102, "realli": [85, 86, 92, 96], "reason": [25, 84, 85, 96, 97], "reassign": 54, "rebas": 85, "recal": 56, "receiv": [24, 43, 50, 97], "recent": [89, 110], "recipi": 97, "recogn": 33, "recommend": [83, 86, 87, 88, 89, 90, 91, 94, 96, 100, 102, 103, 107, 110], "recon": [83, 85, 86, 88, 89, 91, 92, 94, 96, 99, 100, 101, 108], "recon_surf": [81, 89, 94, 110], "reconstruct": [87, 88, 94, 99, 100, 109, 110], "reconstructioni": 109, "record": [104, 107], "recreat": 85, "redistribut": 97, "reduc": [34, 41, 45, 54, 85, 90, 92, 103], "reduce_to_aseg": 81, "reducelronplateau": [28, 106], "reducelronplateauwithrestart": 28, "reduct": 41, "ref_img": 62, "refer": [20, 25, 28, 30, 47, 62, 75, 88, 91, 95, 109, 110], "referenc": 47, "reflect": 32, "reg": [70, 73, 88], "reg_mod": [66, 83, 88, 107], "regard": [84, 97], "regardless": 84, "region": [20, 44, 47, 67, 78, 79, 102], "region_label": 44, "regist": [69, 83, 87, 88, 90, 91, 98, 107, 110], "registr": [66, 69, 87, 88, 90, 92, 95, 98, 107, 110], "registri": 94, "regroup": 14, "regular": [88, 90], "reject": 84, "rel": [49, 50, 58, 100, 111], "relabel": 15, "relat": [14, 44, 100], "releas": [34, 94, 98, 110], "relev": [33, 47, 85, 86, 88], "reliabl": [25, 83, 85, 88, 90, 96, 109], "religion": 84, "relu": [24, 43], "remain": [34, 97], "remap": [15, 34, 62], "remot": 85, "remov": [20, 34, 47, 48, 49, 78, 84, 87, 92, 94, 99, 102, 103, 105, 107, 111], "remove_ckpt": 49, "remove_suffix": [58, 102, 103], "renam": 76, "render": [92, 94], "reorder": 33, "reorient": [15, 33, 62], "reorient_img": 62, "repeat": 79, "repercuss": 84, "replac": [23, 34, 42, 58, 78, 86, 88, 89, 94, 98, 110, 111], "replace_label": 78, "replic": 47, "repo": [85, 89], "report": [84, 91, 95], "report_empti": 47, "repositori": [85, 89, 102, 107], "repres": [15, 38, 42, 43, 45, 49, 50, 65, 84, 90, 97, 99], "represent": 84, "repro": 85, "reproduc": [85, 97, 111], "reproduct": [85, 97], "request": [41, 42, 50, 65, 85, 86, 100, 102], "requir": [20, 33, 47, 50, 53, 70, 83, 86, 94, 95, 97, 99, 100, 103, 106, 109, 111], "require_measurefil": 47, "require_pvfil": 47, "rerun": 100, "resafe_surfac": [75, 76], "resampl": [33, 83, 103], "rescal": [33, 62, 65, 66, 67], "rescale_imag": 62, "research": [83, 88, 96, 109, 110], "reserv": 89, "reset": [29, 30, 55, 56, 85], "resiz": [20, 65], "reslic": 33, "resolut": [14, 39, 63, 64, 66, 83, 88, 96, 107, 109, 110, 112], "resolv": [50, 85, 86, 93], "resourc": [87, 88, 89, 94, 98, 99, 100, 110], "respect": [30, 31, 40, 47, 56, 84, 87, 94, 100, 110], "respons": [93, 95, 97], "restart": 28, "result": [29, 30, 31, 33, 34, 41, 47, 50, 59, 66, 84, 86, 88, 89, 90, 91, 92, 96, 97, 102, 103, 107, 109, 110, 111], "result_path": 13, "resum": [26, 49], "resume_experi": [26, 49], "retain": [24, 43, 97], "retcod": 59, "retrain": 107, "retriev": [28, 50, 63], "return": [14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31, 33, 34, 35, 36, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53, 54, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 73, 74, 75, 76, 77, 78, 79, 80, 94], "return_bord": 20, "return_map": 47, "returncod": 80, "reus": [90, 110], "reuter": [83, 84, 88, 90, 96, 107, 109, 110], "rev_map": 73, "revers": 62, "reversed_dict": 54, "revert": 110, "review": 84, "revis": [97, 111], "rewrit": [75, 76, 85], "rewrite_mc_surfac": 81, "rewrite_oriented_surfac": 81, "rewritten": 76, "rgba": [54, 78], "rh": [34, 70, 86, 91, 105], "rhcerebralwhitematt": 111, "rhcortex": 111, "rhsurfacehol": 111, "ribbon": [88, 110], "right": [15, 21, 34, 38, 44, 53, 61, 69, 84, 87, 91, 97, 99, 105], "rigid": [68, 69], "risk": 97, "rm": [87, 89, 92, 94, 110], "rmat2angl": 68, "rmax": 34, "rmin": 34, "rng_seed": 106, "robust": [14, 33, 47, 66, 86, 88, 90, 107, 111], "robust_percentag": 47, "robust_voxel_count": 47, "robustli": [33, 90], "rocm": [89, 94], "roi": [16, 83, 110], "root": [49, 50, 58, 61, 87, 88, 94, 100], "rosa": [88, 90, 109], "rotat": [14, 68, 77, 107], "rotate_spher": 81, "round": 33, "row": [14, 47, 100], "royalti": 97, "rtx": 92, "run": [22, 25, 39, 46, 50, 61, 63, 64, 66, 80, 83, 85, 86, 89, 91, 92, 95, 96, 98, 99, 102, 103, 104, 106, 108, 110, 111], "run_fastsurf": [86, 87, 88, 89, 90, 92, 98, 99, 102, 103, 107, 109, 110], "run_model": [46, 108, 112], "run_predict": [81, 88, 94, 101, 108], "run_tool": [61, 81], "runmodelondata": 46, "runner": [49, 88, 102, 103, 106, 107, 109], "runtim": [59, 85], "runtimeerror": [20, 34, 47, 50, 54, 58, 66], "rusiel": 90, "sabuncu": 90, "safe": [88, 94], "sag_mask": 105, "sagitt": [15, 34, 38, 39, 46, 62, 66, 102, 103, 105, 106, 107], "sagittal_coronal_remap_lookup": 34, "sagittal_lut_dict": 34, "sai": 100, "same": [14, 15, 20, 23, 30, 42, 47, 54, 61, 70, 73, 78, 80, 85, 86, 87, 88, 89, 90, 92, 94, 99, 100, 102, 103, 106, 107, 110, 111], "sampl": [14, 32, 78], "sample_img": 78, "sample_intensity_stats_from_imag": 14, "sample_nearest_nonzero": 78, "sample_parc": 81, "santiago": 107, "save": [13, 21, 26, 31, 34, 46, 49, 57, 72, 75, 79, 86, 87, 88, 90, 98, 102, 103, 107, 110, 111], "save_a": [34, 46], "save_checkpoint": [26, 49], "save_imag": 34, "save_img": 46, "save_mgh_imag": 21, "save_nii_imag": 13, "save_path": [13, 21], "sbom": 94, "scale": [14, 33, 39, 42, 63, 64, 65, 66, 106, 111], "scale_factor": [42, 65], "scale_factor_out": [42, 65], "scalecrop": 33, "scan": 14, "scanner": 96, "scannerra": 75, "scenario": [92, 111], "scene": 95, "schedul": [26, 28, 49, 53, 87, 99, 100, 106], "schedular": 53, "scheme": [86, 107], "schmanski": [88, 90, 109], "scipi": 30, "scope": [85, 95], "score": [29, 30, 55, 56], "screen": 94, "script": [25, 33, 46, 47, 61, 85, 86, 87, 88, 89, 90, 91, 94, 96, 98, 99, 100, 102, 103, 104, 106, 107, 109, 110, 111], "sd": [86, 87, 88, 89, 90, 92, 94, 98, 99, 100, 102, 103, 107, 109, 110, 111], "sdir": [88, 110], "sdk": 85, "se": [102, 103], "search": [26, 41, 47, 49, 50, 61, 78, 85, 88, 100, 102, 103, 109], "search_pattern": 38, "search_tag": [58, 102, 103], "sec": 92, "seccomp": [89, 94], "second": [14, 50, 59, 65, 86, 87, 89, 92, 100, 102, 103, 107, 111], "secondari": 86, "section": [61, 85, 88, 90, 92, 97], "secur": [89, 94, 95], "see": [44, 61, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 94, 96, 98, 99, 100, 102, 103, 106, 109, 110], "seed": [14, 86, 106], "seem": [85, 89], "seg": [47, 69, 78, 83, 87, 88, 91, 100, 103, 107], "seg_": 100, "seg_arrai": 44, "seg_bord": 47, "seg_dst": 69, "seg_input": 88, "seg_log": [88, 102, 103, 107], "seg_mean": [47, 111], "seg_mov": 69, "seg_onli": [83, 86, 87, 88, 89, 90, 91, 92, 100, 109, 110], "seg_output": 88, "segdir": 110, "segemnt": [88, 109], "segfil": [47, 50, 111], "segid": 47, "segmap": 21, "segment": [14, 15, 23, 25, 29, 30, 33, 34, 38, 42, 44, 45, 46, 47, 50, 66, 67, 69, 74, 89, 90, 94, 95, 96, 98, 99, 100, 102, 103, 105, 106, 107, 109, 110, 111], "segstat": [81, 101, 108], "segstatsfil": [47, 111], "select": [21, 66, 69, 83, 88, 91, 94, 100, 102, 103, 106, 107, 111], "self": 94, "sell": 97, "semi": [43, 89], "send": [80, 100], "sensit": [90, 96], "sensitivii": 90, "sent": [94, 97], "separ": [47, 54, 71, 84, 87, 97, 99, 100], "sequenc": [14, 20, 30, 47, 54, 96], "sequenti": [34, 87, 88, 109], "seri": [99, 110], "serial": [50, 100], "serialexecutor": 50, "serv": 47, "server": 49, "servic": 97, "set": [16, 28, 30, 31, 33, 34, 38, 39, 46, 50, 52, 54, 56, 57, 62, 64, 65, 66, 68, 75, 76, 79, 84, 87, 88, 89, 92, 98, 99, 102, 103, 105, 106, 107, 109, 110, 111], "set_and_create_outdir": 46, "set_cfg": [39, 64], "set_devic": [30, 56], "set_lr": 28, "set_model": [46, 64], "set_plan": 16, "set_subject": 46, "set_summary_path": 31, "set_up_cfg": [46, 66], "set_up_model_param": 46, "setter": 46, "setup": [86, 88, 89, 90, 110], "setup_log": 52, "setup_model": [39, 64], "setup_opt": [25, 80], "setupfreesurf": [86, 87, 90, 110], "sever": [87, 94, 96], "sex": 84, "sexual": 84, "sform": 33, "sgd": 106, "sh": [86, 87, 88, 89, 90, 92, 94, 98, 101, 102, 103, 107, 108], "shall": [96, 97], "shape": [15, 20, 33, 41, 42, 47, 65, 66, 68, 78, 79], "share": [14, 47, 50, 97], "shell": 94, "shift": 33, "shm": 89, "should": [14, 15, 20, 30, 33, 34, 45, 47, 56, 57, 58, 61, 64, 65, 68, 69, 70, 71, 79, 85, 86, 87, 88, 89, 94, 96, 98, 100, 102, 103, 105, 107, 111], "show": [84, 85], "shown": 91, "shrink": 67, "shrunk": 47, "sid": [58, 66, 73, 86, 87, 88, 89, 90, 92, 94, 98, 99, 100, 102, 103, 107, 109, 110, 111], "side": [20, 85, 95], "sif": [87, 89, 90, 92, 98, 100, 110], "sigma": 43, "sign": 94, "signatur": [30, 56], "significantli": 87, "silicon": [88, 89, 94], "similar": [14, 30, 33, 47, 59, 86, 88, 89, 90, 99, 102, 103, 110], "similarli": [13, 85, 89, 94], "simpl": 47, "simpler": 45, "simpli": [85, 92, 94, 98], "simplifi": [87, 88, 91, 107, 110], "sinc": [85, 88, 89, 94, 98, 102, 103], "singl": [16, 30, 39, 48, 64, 87, 94, 96, 102, 107, 111, 112], "singular": [90, 95, 96, 99, 100], "singularity_imag": [87, 100], "site": 49, "sitk": [67, 69], "situat": [90, 102, 107], "six_connect": 47, "size": [14, 20, 31, 32, 33, 34, 38, 39, 46, 47, 48, 50, 64, 66, 73, 84, 86, 88, 89, 92, 102, 103, 105, 106, 107, 109, 110, 111], "size_averag": 41, "skip": [23, 24, 42, 43, 47, 61, 83, 86, 88, 99, 100, 107, 110], "skip_cleanup": 100, "skull": [86, 90], "slice": [15, 16, 20, 23, 33, 34, 38, 42, 47, 69, 88, 105, 106], "slice_lia2ra": 15, "slice_ras2lia": 15, "slice_thick": [16, 34, 38], "slicer": 47, "slicer_large_patch": 47, "slicer_large_to_patch": 47, "slicer_large_to_smal": 47, "slicer_patch": 47, "slicer_small_to_patch": 47, "slicingsequ": 47, "slicingtupl": 47, "slide": 94, "slightli": [30, 90], "slow": [89, 102, 103, 107], "slower": [88, 89, 92, 96, 110], "slurm": [95, 99, 108], "slurm_array_task_count": 99, "slurm_array_task_id": 99, "slurm_jobarrai": 100, "slurm_task_id": 99, "small": [30, 33, 34, 47, 85, 86, 87, 92, 110], "smaller": [21, 33, 44, 79, 88, 90, 94, 100, 111], "smallest": [33, 88, 111], "smooth": [78, 79, 90], "smooth_aparc": 81, "smoothed_label": 79, "snapshot": [66, 88, 107], "snapshott": 94, "snippet": 100, "so": [15, 20, 26, 34, 49, 50, 58, 67, 70, 73, 79, 85, 87, 88, 89, 91, 92, 94, 96, 98, 99, 100, 110], "social": 84, "socioeconom": 84, "softmax": 65, "softwar": [89, 91, 94, 96, 97], "sole": [85, 97], "solut": [68, 83, 88, 94, 96, 109, 110], "solv": [85, 89], "some": [85, 86, 89, 91, 94, 95, 110], "somefold": 100, "someon": 85, "sometim": [33, 86], "sourc": [13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 86, 87, 88, 89, 90, 94, 96, 97, 103, 106, 107, 110], "source_intens": 67, "source_shap": 16, "source_spac": 54, "space": [15, 20, 30, 33, 34, 47, 54, 62, 67, 69, 78, 84, 87, 88, 90, 109, 111], "spars": [78, 79], "spatial": [23, 42], "spatialimag": [33, 34, 46, 47], "spatiotempor": 90, "spec": 89, "special": [97, 102], "specif": [20, 30, 33, 38, 39, 47, 49, 56, 84, 86, 87, 88, 91, 94, 96, 98, 99, 100, 102, 103, 105, 107, 110], "specifi": [14, 20, 28, 30, 33, 46, 47, 54, 65, 66, 70, 87, 88, 94, 98, 99, 102, 103, 104, 106, 107, 110, 111], "spectral": [88, 110], "speed": [87, 88, 92, 102, 103, 107, 110], "sphere": [21, 70, 73, 77, 88], "spheric": [21, 88, 90, 110], "spherical_wrapp": 80, "spherically_project_wrapp": 81, "split": [31, 34, 99], "split_cortex_label": 34, "splot": 34, "spm": 86, "sqr": 47, "sqrt": 47, "squar": [47, 68], "squeue": 100, "src": [33, 49, 69, 70, 73, 88, 102, 103, 106, 107, 109], "src_dir": 70, "src_fname": 72, "src_header": 72, "src_label": 70, "src_label_nam": 73, "src_min": 33, "src_sphere": 73, "src_sphere_nam": 70, "srcsphere": 70, "srun_fastsurf": [87, 108], "ssl": 94, "stabil": 47, "stabl": [28, 30, 85, 87, 89], "stack": [20, 34, 85], "stage": [28, 86], "stai": [58, 73, 83, 96], "standard": [26, 32, 33, 49, 63, 88, 94, 95, 100, 102, 103, 107, 110], "start": [41, 47, 87, 89, 94, 95, 96, 99, 100, 110], "startup": [92, 99], "stat": [14, 29, 47, 86, 87, 88, 90, 91, 92, 96, 102, 107, 110, 111], "state": [26, 30, 49, 64, 97, 100], "statement": 97, "statist": [14, 47, 55, 83, 87, 88, 89, 91, 92, 95, 96, 107, 110, 111], "statsfield": 102, "statsfil": 92, "statu": [61, 84, 88, 100], "statusfil": 99, "std": [14, 32], "stddev": 47, "stderr": 59, "stdin": 99, "stdout": [33, 34, 59, 61, 94, 103], "step": [28, 29, 57, 85, 86, 87, 88, 89, 90, 100], "step_lr": 106, "steplr": 53, "still": [90, 110], "stool": [99, 100], "stop": [34, 70, 87], "stop_miss": 70, "stoppag": 97, "storag": [94, 100], "store": [18, 19, 20, 47, 66, 73, 87, 88, 89, 102, 103, 107, 110], "store_talairach": [18, 19], "store_tru": 58, "str": [13, 15, 19, 20, 25, 26, 30, 31, 32, 34, 36, 38, 39, 46, 47, 48, 49, 50, 51, 52, 54, 56, 57, 58, 61, 63, 64, 65, 66, 67, 70, 71, 72, 73, 75, 76, 78, 79, 80, 88, 103], "strand": [34, 38, 105], "strategi": [14, 20], "stream": [88, 90, 92, 96], "strenght": 96, "strict": 33, "strictli": 14, "stride": 106, "stride_conv": [24, 43, 106], "stride_pool": [24, 43, 106], "string": [15, 33, 34, 39, 47, 48, 50, 61, 66, 70, 71, 73, 94, 100], "strip": [86, 90, 103], "strong": [85, 86], "strongli": 94, "structnam": 47, "structur": [14, 34, 47, 83, 86, 88, 90, 91, 96, 107, 109, 110, 111], "stub": 102, "studi": [90, 99, 100], "style": [34, 61, 88, 103, 105, 110], "sub": [25, 26, 47, 49, 83, 88, 91, 92, 96, 100, 102, 103, 107, 109], "sub_modul": 81, "sub_patch": 47, "sub_region": 47, "subcort": [86, 91], "subcortgrai": 111, "subdirectori": 100, "subfield": [96, 107], "subfold": [86, 96, 110], "subject": [16, 19, 35, 38, 46, 47, 50, 64, 66, 70, 73, 88, 90, 94, 95, 97, 98, 100, 102, 105, 107, 108, 109, 111], "subject1": 87, "subject10": 87, "subject2": 87, "subject3": 87, "subject_dir": [38, 50, 86], "subject_id": [47, 99, 100, 110, 111], "subject_id1": [87, 100], "subject_list": [87, 99, 100, 110], "subject_list_awk_code_arg": 100, "subject_list_awk_code_sid": 100, "subject_list_awk_code_t1": 100, "subject_list_delim": 100, "subject_nam": [63, 64, 66], "subject_path": 16, "subject_success": 100, "subjectdataset": 16, "subjectdirectori": [46, 50], "subjectdirectoryconfig": 58, "subjectid": [88, 110], "subjectlist": [46, 50, 58], "subjectload": 19, "subjects_dir": [47, 86, 88, 90, 109, 110, 111], "subjects_list": [18, 87, 110], "subjectx": [89, 94, 95, 98, 103], "subjid": 85, "sublicens": 97, "submiss": 97, "submit": [34, 50, 97, 100], "subpars": 111, "subparser_callback": 47, "subpatch": 47, "subprocess": 59, "subregion": 47, "subseg": [20, 62], "subsegment": 83, "subsequ": 97, "subset": [85, 87], "substitut": 88, "substructur": 83, "subtl": 90, "subtract": 20, "succe": 100, "succeed": [34, 38, 105], "success": [25, 47, 61, 66, 86, 87, 94, 99], "successfulli": [89, 99, 100], "sudo": 89, "sudr": 14, "suffici": [89, 99], "suffix": [34, 50, 88, 102, 103, 105, 107, 110, 111], "suggest": 95, "suitabl": 33, "sulci": [34, 38, 105], "sulcu": 34, "sum": [47, 56], "sum_of_intens": 47, "sum_of_intensity_squar": 47, "summari": [29, 31, 55, 91, 111], "sums_of_squar": 47, "super": 92, "supersed": 97, "suppli": 30, "support": [34, 47, 53, 58, 65, 83, 86, 88, 95, 96, 97, 99, 102, 109, 110], "supported_output_file_format": 34, "supratentori": 111, "supratentorialnotv": 111, "supratentorialnotventvox": 111, "sure": [75, 85, 87, 89, 94, 98, 110], "surf": [73, 78, 79, 83, 85, 86, 87, 88, 89, 91, 92, 94, 96, 100, 101, 108], "surf_": 100, "surf_ctab": 78, "surf_label": 78, "surf_lut": 78, "surf_nam": 78, "surf_onli": [83, 86, 88, 90, 100, 109, 110], "surf_xxx_yi": 100, "surf_xxx_yy_zz": 100, "surfac": [30, 70, 73, 75, 76, 78, 79, 87, 89, 90, 92, 94, 95, 96, 98, 99, 100, 101, 108, 109], "surface_backup": 76, "surface_fil": 76, "surfacehol": 111, "surfacera": 75, "surfer": [86, 87, 88, 92, 98, 110], "surflut": 78, "surviv": 90, "switch": [85, 88, 91, 92, 96, 98, 110], "symbol": 91, "symlink": [86, 91, 96], "symmetr": [30, 78, 79], "synchron": 46, "sys_ptrac": 89, "system": [68, 87, 94, 95, 97, 98, 99, 102, 103, 107, 110], "systemat": 86, "t": [14, 68, 69, 72, 85, 87, 89, 92, 103, 110], "t1": [13, 39, 63, 66, 86, 87, 88, 89, 90, 92, 94, 96, 98, 99, 100, 102, 103, 107, 109, 110, 111], "t1_1": [90, 109], "t1_2": [90, 109], "t1_input": [88, 110], "t1_path": [66, 100], "t1t2": [63, 64, 66], "t1w": [83, 88, 90, 99, 100, 107], "t2": [63, 66, 83, 88, 91, 99, 107, 109], "t2_input": 88, "t2_nu": 91, "t2_nu_reg": 91, "t2_path": 66, "t2tot1": 107, "t2w": [83, 99, 107], "t_0": 28, "t_addarg": 58, "t_mult": 28, "t_othervalu": 54, "tab": 54, "tabl": [20, 34, 47, 62, 73, 78, 91, 103, 105, 111], "table_to_datafram": 47, "tabular": 91, "tag": [85, 89, 94, 98, 102, 103], "tag_nam": 94, "take": [14, 65, 75, 76, 84, 87, 88, 92, 94, 109, 110], "taken": [70, 73, 88, 90], "tal": 67, "tal_reg": [88, 92], "talairach": [19, 67, 87, 88, 92, 95, 98, 110], "talk": 85, "target": [15, 20, 33, 41, 54, 66, 67, 69, 70, 73, 85, 88, 94, 99, 110], "target_bg": 67, "target_dtyp": 48, "target_img_s": 20, "target_intens": 67, "target_shap": [16, 20, 40, 66], "target_slic": 47, "target_spac": 54, "target_wm": 67, "targetdir": 110, "team": [84, 85], "tech": 94, "technic": 86, "tell": [87, 88, 96, 98], "temp": 57, "temp_competit": 103, "templat": [88, 90, 109, 110], "templateid": [90, 109], "tempor": 90, "temporari": 84, "temporarili": 84, "tensor": [14, 20, 23, 24, 29, 30, 32, 34, 39, 40, 41, 42, 43, 45, 46, 47, 55, 56, 57, 63, 64, 65, 66], "term": 97, "termin": [59, 88, 89, 97, 100, 110], "test": [17, 36, 50, 85, 87, 88, 89, 92, 94, 96, 110], "test_subject": [88, 107], "test_subject_t1": 88, "test_subject_t1_bias_field_correct": 107, "test_subject_t2_bias_field_correct": 107, "test_subject_t2_bias_field_corrected_and_coregistered_to_t1": 107, "testload": 16, "testmet": 29, "text": [47, 50, 58, 61, 88, 91, 92, 97, 108], "textio": 61, "th": [34, 99], "thalamu": 96, "than": [33, 44, 48, 68, 87, 88, 89, 92, 94, 99, 100, 111], "thank": [86, 93], "thei": [66, 73, 84, 85, 87, 94, 98, 107], "them": [66, 86, 87, 89, 96, 99, 104, 110], "theoret": 90, "theori": 97, "therapi": 90, "therebi": 75, "therefor": [30, 86, 90, 94, 96, 99, 107], "therein": 61, "thereof": 97, "thi": [14, 15, 20, 25, 26, 30, 31, 33, 34, 38, 39, 44, 45, 46, 47, 49, 50, 54, 56, 58, 61, 62, 64, 65, 66, 74, 75, 78, 79, 81, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 94, 96, 97, 98, 99, 100, 102, 103, 104, 105, 107, 109, 110, 111], "thick": [15, 34, 83, 86, 88, 90, 91, 92, 96, 105, 106, 110], "thick_slic": 15, "thing": [85, 89], "think": 96, "third": 97, "thoroughli": [89, 96], "those": [85, 86, 94, 96, 97, 98], "thousandth": 33, "thre": [44, 67], "thread": [22, 46, 47, 50, 64, 66, 81, 86, 87, 88, 94, 99, 102, 103, 107, 110, 111], "threadpoolexecutor": [34, 59], "threads_seg": [88, 99], "threads_surf": [88, 99], "threaten": 84, "three": [33, 34, 87, 91, 99, 100], "thresh": 70, "threshold": [15, 20, 33, 34, 38, 44, 46, 47, 67, 103, 105], "through": [33, 42, 43, 65, 85, 89, 90, 94, 97, 99, 106], "throughout": 83, "thu": [33, 94], "tid": [90, 109], "tid1": [90, 109], "tid2": [90, 109], "tidn": 90, "time": [34, 61, 83, 85, 86, 87, 88, 89, 90, 92, 94, 99, 100, 109, 110], "time_seg": 100, "time_surf": 100, "timelimit": 100, "timeout": [50, 59], "titan": 92, "titl": [31, 57, 85, 93, 97], "tl": 94, "tmp": 86, "tmult": 28, "to_same_typ": 54, "toch": 39, "togeth": [59, 99], "toml": [61, 94], "tool": [86, 90, 96, 99, 100, 102], "toolbox": 90, "toolchain": 89, "toolkit": 89, "top": [34, 47, 92, 110], "top_left": [32, 40, 65], "top_right": 65, "torch": [20, 26, 28, 29, 30, 34, 36, 39, 41, 45, 46, 49, 50, 53, 55, 56, 57, 63, 64, 65], "torchio": 14, "tort": 97, "total": [14, 41, 44, 55, 60, 86, 88, 92, 100, 102, 103, 107], "total_epoch": [29, 55], "total_it": [29, 55], "total_thread": 99, "totalgrai": 111, "totensor": [14, 32], "totensortest": [14, 32], "toward": [20, 24, 43, 84], "tp": [56, 57], "tpid": [90, 109], "tqdm": 99, "tqdm_disabl": 99, "trace": 85, "traceback": 85, "track": [46, 55, 85, 97], "tracker": 85, "tract": 83, "tracula": 96, "trade": [94, 97], "trademark": 97, "tradit": [83, 110], "trail": 48, "train": [17, 26, 28, 29, 36, 49, 55, 57, 88, 102, 105, 112], "training_sagittal_single_resolut": 106, "trajectori": 28, "transfer": [97, 98, 99], "transform": [14, 15, 16, 20, 30, 34, 35, 38, 54, 56, 62, 63, 66, 67, 68, 69, 72, 86, 87, 97, 107], "transform_axi": [15, 34], "transform_axial2coron": 62, "transform_axial2sagitt": [15, 62], "transform_coron": 15, "transform_sagitt": [15, 34], "transit": 83, "translat": [14, 97, 106], "transpos": [23, 42], "travers": 94, "treat": [47, 90], "tree": 73, "trg": [33, 69, 70, 73], "trg_label": 73, "trg_sid": [70, 73], "trg_sphere": 73, "trg_sphere_nam": 70, "trg_surf": 73, "trg_valu": 73, "trg_white": 70, "trg_white_nam": 70, "trgsphere": 70, "tri": [60, 90], "tria": [78, 79], "triangl": [76, 78, 79], "trick": 94, "trigger": 47, "troll": 84, "true": [14, 15, 24, 33, 34, 43, 47, 54, 56, 62, 69, 70, 71, 79, 94, 106], "true_cl": 56, "truth": [29, 34, 38, 56, 105], "try": [50, 85, 89, 96, 99, 110], "tsqrt": 69, "tsv": [54, 103, 105], "tsvlookupt": 54, "tune": [26, 49, 83, 91, 96], "tupl": [13, 16, 30, 31, 32, 33, 34, 39, 46, 47, 54, 56, 64, 65, 66, 67, 71, 73, 78], "turn": [33, 38, 105], "tutori": 86, "tutorial_data": 92, "tutorial_subj": 92, "twice": 89, "twitter": [83, 96], "two": [30, 32, 47, 65, 68, 83, 89, 90, 91, 94, 99, 100], "txt": [44, 87, 88, 89, 90, 94, 98, 103, 106, 110], "type": [15, 20, 30, 32, 33, 34, 46, 47, 48, 49, 54, 58, 78, 85, 94, 97, 107, 110], "type_hint": 54, "typeerror": 20, "typic": [47, 88], "u": [83, 85, 87, 89, 92, 94, 96, 100, 110], "uchar": [33, 34, 88, 110], "uint8": 33, "unaccept": 84, "unbias": [88, 90, 109], "unchang": 99, "unconfin": [89, 94], "undefin": [54, 86], "under": [34, 86, 87, 88, 89, 92, 94, 97, 98, 102, 103, 110], "underneath": 99, "undersegment": 86, "understand": [85, 86], "understood": 90, "undesir": [88, 109], "undetermin": 34, "undo": 47, "ungrow": 47, "unifi": 35, "uniform": 47, "uniform_filt": 47, "unify_img": 35, "unify_lateralized_label": 34, "union": [26, 30, 32, 33, 34, 39, 46, 47, 48, 49, 53, 56, 58, 70, 73, 97], "uniqu": 111, "unit": [30, 47, 111], "uniti": 30, "univari": 90, "universal_newlin": 59, "unknown": [21, 34, 71, 78], "unknown_label": 34, "unknown_mask": 21, "unless": [91, 94, 97, 99], "unlik": 33, "unlimit": 59, "unpool": [23, 24, 42, 43], "unquot": 48, "unquote_str": 48, "unreli": [86, 96], "unsid": 79, "unsuccess": 100, "until": [46, 85, 90, 100], "unwelcom": 84, "up": [20, 33, 34, 39, 42, 43, 46, 52, 62, 64, 65, 66, 78, 83, 85, 87, 88, 92, 100, 102, 103, 107, 110], "updat": [21, 28, 29, 30, 31, 39, 47, 54, 55, 56, 57, 64, 83, 85, 86, 89, 91, 93, 96, 100], "update_num_step": 57, "update_results_dir": 31, "update_split_path": 31, "update_stat": [29, 55], "update_structnam": 47, "upgrad": 89, "upinterpol": 43, "upon": [25, 107], "upright": 69, "upstream": 85, "url": [49, 66, 104], "us": [13, 14, 15, 20, 26, 28, 29, 30, 33, 34, 38, 39, 42, 46, 47, 49, 50, 54, 56, 58, 62, 64, 65, 66, 83, 84, 85, 87, 88, 89, 90, 91, 92, 93, 94, 95, 97, 98, 99, 100, 102, 103, 104, 105, 106, 107, 109, 110, 111], "usabl": 60, "usag": [30, 39, 46, 56, 88, 95, 102, 103, 104, 105, 106, 108, 111], "usecas": 94, "used_label": 47, "user": [50, 58, 85, 87, 88, 89, 90, 92, 94, 98, 100, 110], "usernam": 85, "usual": [15, 30, 59, 73, 78, 79, 85, 88, 90, 94, 98, 99, 110], "util": [36, 61, 81, 108], "v": [87, 89, 92, 94, 98, 110], "v0": 94, "v2": 94, "v5": 89, "v_dst": 77, "v_mov": 77, "val": [17, 36, 48], "val_load": [39, 64], "valid": [29, 31, 39, 48, 50, 55, 57, 61, 64, 87, 89, 96, 98, 99, 106], "validation_sagittal_single_resolut": 106, "valu": [14, 20, 26, 28, 29, 30, 33, 34, 39, 41, 44, 45, 46, 47, 48, 49, 50, 54, 55, 56, 57, 58, 61, 67, 69, 70, 73, 78, 79, 85, 86, 88, 94, 99, 105, 106, 111], "valueerror": [20, 47, 53, 54, 65, 66, 67, 68, 70, 72, 73], "var": [88, 94, 109, 110], "vari": 89, "variabl": [41, 87, 88, 89, 94, 98, 99, 109], "varianc": 90, "variou": [86, 89, 104], "vent_label": 44, "ventricl": [34, 44, 83], "ventriclechoroidvol": 111, "venv": 89, "verbal": 97, "verbos": [33, 70], "veri": [47, 86, 89, 90, 94, 96, 110, 111], "versa": [47, 62], "version": [33, 71, 81, 84, 85, 86, 87, 88, 91, 92, 94, 95, 97, 98, 99, 100, 107, 110], "version_lin": 61, "version_tag": 94, "versiondict": 61, "vertex": [47, 73, 75, 78, 79, 90, 91], "vertic": [73, 77, 78, 79], "vessel": 34, "vetric": 73, "via": [47, 70, 78, 79, 84, 85, 86, 88, 89, 90, 94, 95, 98, 100, 102, 103, 109, 110, 111], "vice": [47, 62], "video": [89, 94, 99], "vidx": 78, "view": [20, 23, 33, 39, 42, 64, 66, 88, 96, 102, 103, 107], "view_op": 46, "view_opt": 66, "viewagg_devic": [22, 46, 58, 64, 66, 88, 96, 99, 102, 103, 107], "viewer": 92, "viewgg_devic": 107, "viewoper": 66, "viewpoint": 84, "vinn": [63, 104, 110], "violat": 33, "virtual": [47, 111], "virtuallabel": 47, "visibl": [87, 94, 98, 110], "visual": [29, 89, 92, 96, 107], "visualize_batch": 31, "vol": [15, 34, 62], "volum": [14, 15, 20, 30, 34, 44, 47, 62, 66, 75, 78, 83, 86, 87, 88, 91, 92, 96, 102, 103, 110, 111], "volume_mm3": 47, "volume_precis": [47, 111], "volume_similar": 30, "volumetr": 83, "vote": 79, "vox": 48, "vox2ra": 69, "vox2vox": 33, "vox_coord": 78, "vox_origin": 67, "vox_siz": [33, 34, 46, 48, 88, 100, 103], "vox_vol": 47, "voxel": [15, 20, 21, 33, 34, 38, 44, 47, 48, 67, 69, 78, 86, 88, 92, 103, 105, 110, 111], "voxel_count": 47, "voxels": 103, "voxelspac": 30, "voxsizeopt": [33, 34], "voxvol": 44, "vt": 54, "vulner": 95, "w": [15, 41, 42, 43, 86], "w6600": [89, 94], "wa": [14, 26, 38, 49, 50, 61, 75, 76, 84, 86, 87, 88, 89, 94, 97, 98, 100, 105], "wai": [33, 85, 87, 89, 90, 91, 92, 99, 100], "wait": [50, 59, 80, 90], "walk": 89, "want": [30, 47, 56, 85, 87, 89, 92, 98, 99, 110], "warm": 28, "warmup": 28, "warmup_factor": 28, "warmup_it": 28, "warmup_method": 28, "warmupcosinelr": 28, "warn": [34, 70, 81], "warp": 13, "warp_path": 13, "warranti": 97, "watersh": 86, "we": [14, 21, 33, 47, 50, 68, 70, 84, 85, 86, 88, 89, 90, 91, 92, 94, 96, 98, 99, 102, 103, 107, 110], "web": 85, "websit": [87, 98], "weigh": [63, 94], "weight": [13, 14, 15, 23, 31, 32, 34, 35, 38, 41, 42, 47, 63, 65, 87, 90, 92, 94, 96, 98, 100, 103, 105, 110], "weight_c": 41, "weight_dic": 41, "weight_factor": 65, "weight_vol": 34, "welcom": 84, "well": [47, 85, 86, 87, 88, 89, 90, 92, 94, 96, 99, 111], "were": [47, 91, 100], "wget": [89, 94], "whalf": 47, "what": [79, 84, 85, 87, 89, 95, 100], "when": [14, 20, 30, 33, 46, 65, 70, 78, 84, 87, 90, 94, 95, 98, 99, 102, 103, 107, 111], "whenev": 91, "where": [13, 14, 15, 20, 28, 29, 30, 45, 47, 54, 58, 62, 66, 69, 70, 73, 78, 79, 87, 88, 89, 90, 94, 97, 98, 99, 100, 102, 103, 107, 109, 110], "wherev": 97, "whether": [14, 15, 19, 26, 33, 34, 44, 47, 48, 49, 50, 54, 61, 66, 70, 76, 85, 86, 88, 97, 100, 111], "which": [14, 21, 23, 28, 30, 33, 34, 42, 46, 47, 49, 58, 59, 61, 66, 70, 73, 78, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 94, 96, 97, 98, 99, 100, 102, 103, 105, 107, 110, 111], "while": [50, 58, 85, 86, 97, 100], "white": [14, 34, 45, 67, 70, 73, 91, 95], "white_check_mark": 93, "whitematteredits_freeview": 86, "who": [84, 94, 110], "whole": [46, 83, 86, 96, 97, 107, 110], "whom": 97, "whose": [44, 54, 106], "why": [85, 89, 94, 96, 98], "wide": 47, "wider": 79, "width": [13, 39, 42, 47, 64, 65, 69, 106], "wiki": 84, "window": [47, 85, 95], "wise": [31, 41, 83, 91, 110], "wish": 94, "withcc": 91, "within": [83, 84, 88, 90, 92, 94, 96, 97, 103, 106, 109, 110], "without": [34, 38, 48, 70, 81, 84, 86, 87, 91, 92, 94, 97, 99, 100, 105, 107], "wm": [21, 34, 38, 45, 67, 73, 83, 86, 88, 90, 105, 110], "wm_mask": 21, "wm_merge_clean": 81, "wmparc": [91, 96], "wo": 88, "won": 87, "work": [49, 50, 61, 86, 87, 88, 89, 90, 94, 96, 97, 98, 99, 100, 102, 103, 106, 107, 109, 110], "worker": 94, "workload": 87, "workstat": 92, "worldwid": 97, "would": [85, 86, 87, 89, 90, 92, 94, 98, 100], "wrapper": 110, "write": [29, 34, 47, 55, 61, 70, 72, 73, 85, 87, 97, 99, 111], "write_annot": 70, "write_statsfil": 47, "write_summari": [29, 55], "writelta": 72, "writer": [29, 55], "writesurflabel": 73, "written": [70, 73, 87, 94, 97, 98, 102, 103, 107, 111], "wsl": 89, "wsl2": 89, "wt1": 63, "wt2": 63, "www": [84, 97, 111], "x": [23, 24, 30, 34, 41, 42, 43, 56, 65, 83, 89, 93, 96, 102, 103], "x86": 85, "x86_64": 89, "xfm": 86, "xp": 92, "xu": [83, 88, 96, 107, 109], "y": [87, 89], "yac": [26, 31, 36, 39, 41, 42, 46, 49, 51, 53, 57, 64, 65, 66], "yaml": [46, 49, 51, 103, 106, 107], "yet": [85, 87, 89, 90, 100], "yield": [46, 47, 50, 102, 103, 111], "yml": 89, "you": [30, 56, 83, 85, 86, 87, 88, 89, 90, 92, 93, 94, 96, 97, 98, 99, 100, 102, 103, 104, 107, 109, 110], "your": [85, 86, 87, 88, 89, 92, 94, 95, 96, 97, 99, 103, 109, 110], "yourself": [89, 94], "yymmdd": 100, "z": 100, "zenodo": [104, 107], "zero": [14, 20, 32, 33, 47, 48, 56, 73, 78], "zeropad2d": 32, "zeropad2dtest": 32, "zmax": 34, "zmin": 34, "zoom": [38, 39, 46, 63, 64, 66], "zoom2d": [40, 65], "zoom3d": 40, "zuckerberg": [83, 96]}, "titles": ["CerebNet", "CerebNet.dataloader", "CerebNet.datasets", "CerebNet_models", "CerebNet.utils", "FastSurferCNN", "FastSurferCNN.data_loader", "FastSurferCNN.models", "FastSurferCNN.utils", "HypVINN", "HypVINN.data_loader", "HypVINN.models", "HypVINN.utils", "CerebNet.apply_warp", "CerebNet.data_loader.augmentation", "CerebNet.data_loader.data_utils", "CerebNet.data_loader.dataset", "CerebNet.data_loader.loader", "CerebNet.datasets.generate_hdf5", "CerebNet.datasets.load_data", "CerebNet.datasets.utils", "CerebNet.datasets.wm_merge_clean", "CerebNet.inference", "CerebNet.models.networks", "CerebNet.models.sub_module", "CerebNet.run_prediction", "CerebNet.utils.checkpoint", "CerebNet.utils.load_config", "CerebNet.utils.lr_scheduler", "CerebNet.utils.meters", "CerebNet.utils.metrics", "CerebNet.utils.misc", "FastSurferCNN.data_loader.augmentation", "FastSurferCNN.data_loader.conform", "FastSurferCNN.data_loader.data_utils", "FastSurferCNN.data_loader.dataset", "FastSurferCNN.data_loader.loader", "FastSurferCNN.download_checkpoints", "FastSurferCNN.generate_hdf5", "FastSurferCNN.inference", "FastSurferCNN.models.interpolation_layer", "FastSurferCNN.models.losses", "FastSurferCNN.models.networks", "FastSurferCNN.models.sub_module", "FastSurferCNN.quick_qc", "FastSurferCNN.reduce_to_aseg", "FastSurferCNN.run_prediction", "FastSurferCNN.segstats", "FastSurferCNN.utils.arg_types", "FastSurferCNN.utils.checkpoint", "FastSurferCNN.utils.common", "FastSurferCNN.utils.load_config", "FastSurferCNN.utils.logging", "FastSurferCNN.utils.lr_scheduler", "FastSurferCNN.utils.mapper", "FastSurferCNN.utils.meters", "FastSurferCNN.utils.metrics", "FastSurferCNN.utils.misc", "FastSurferCNN.utils.parser_defaults", "FastSurferCNN.utils.run_tools", "FastSurferCNN.utils.threads", "FastSurferCNN.version", "HypVINN.data_loader.data_utils", "HypVINN.data_loader.dataset", "HypVINN.inference", "HypVINN.models.networks", "HypVINN.run_prediction", "recon_surf.N4_bias_correct", "recon_surf.align_points", "recon_surf.align_seg", "recon_surf.create_annotation", "recon_surf.fs_balabels", "recon_surf.lta", "recon_surf.map_surf_label", "recon_surf.paint_cc_into_pred", "recon_surf.rewrite_mc_surface", "recon_surf.rewrite_oriented_surface", "recon_surf.rotate_sphere", "recon_surf.sample_parc", "recon_surf.smooth_aparc", "recon_surf.spherically_project_wrapper", "FastSurfer API", "recon_surf", "Welcome to FastSurfer!", "Contributor Covenant Code of Conduct", "Contributing to FastSurfer", "Manual Edits", "Examples", "FastSurfer Flags", "Installation", "Longitudinal Processing", "Output files", "Quick Start", "Security Policy", "Docker Support", "User Guide", "Introduction to FastSurfer", "FastSurfer License", "Singularity Support", "BATCH: brun_fastsurfer.sh", "SLURM: srun_fastsurfer.sh", "Advanced scripts", "CerebNet: run_prediction.py", "FastSurferCNN: run_prediction.py", "FastSurferCNN: download_checkpoints.py", "FastSurferCNN: generate_hdf5.py", "FastSurferCNN: run_model.py", "HypVINN: run_prediction.py", "Scripts", "LONG: long_fastsurfer.sh", "Surface pipeline: recon-surf.sh", "FastSurferCNN: segstats.py", "FastSurfer Utilities"], "titleterms": {"04": 89, "1": [87, 89, 92, 94, 110], "2": [87, 89, 92, 94, 110], "20": 89, "22": 89, "3": [87, 89, 94, 110], "4": [87, 89, 110], "5": [87, 89], "6": 87, "NOT": 86, "acceler": 89, "acknowledg": [83, 96], "advanc": [94, 101, 102, 107, 111], "ai": 89, "align_point": 68, "align_seg": 69, "also": 46, "amd": [89, 94], "an": 85, "apach": 97, "api": 81, "appl": 89, "apply_warp": 13, "ar": 86, "arg_typ": 48, "argument": [88, 102, 103, 104, 105, 106, 107, 110, 111], "asegdkt_segfil": 86, "attest": 94, "attribut": [84, 85], "augment": [14, 32], "batch": 99, "befor": 85, "behind": 90, "best": [94, 98], "bia": 86, "brun_fastsurf": 99, "bug": 85, "build": [94, 98], "buildkit": 94, "can": 86, "cerebnet": [0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 91, 102], "cerebnet_model": 3, "cfg": 107, "checkpoint": [26, 49, 103, 107], "citat": 107, "click": 92, "cluster": 87, "code": [84, 85], "colab": 92, "command": [103, 106, 111], "commandlin": [103, 104, 105, 106, 111], "common": 50, "complet": 92, "conda": 89, "conduct": 84, "config": 103, "conform": 33, "contribut": 85, "contributor": 84, "correct": 86, "coven": 84, "cpu": [89, 94], "create_annot": 70, "creation": 94, "current": 89, "data": [90, 106], "data_load": [6, 10, 14, 15, 16, 17, 32, 33, 34, 35, 36, 62, 63], "data_util": [15, 34, 62], "dataload": 1, "dataset": [2, 16, 18, 19, 20, 21, 35, 63], "debug": 100, "default": [99, 106, 107], "depend": 89, "detail": 110, "develop": 107, "directori": 103, "do": [85, 86], "docker": [87, 88, 89, 92, 94, 110], "dockerhub": 94, "document": 107, "download_checkpoint": [37, 104], "downstream": 96, "dual": 99, "easi": 92, "edit": 86, "effect": 86, "enforc": 84, "enhanc": 85, "environ": 89, "evalu": 103, "exampl": [87, 94, 103, 106, 110], "experienc": 86, "experiment": [89, 94], "expert": 96, "fastsurf": [81, 83, 85, 87, 88, 89, 92, 94, 96, 97, 98, 107, 112], "fastsurfercnn": [5, 6, 7, 8, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 103, 104, 105, 106, 111], "fastsurfervinn": 106, "field": 86, "file": [91, 107], "final": 90, "flag": [87, 88, 94, 98, 110], "freesurf": [86, 89, 96], "from": 94, "fs_balabel": 71, "full": [88, 103, 104, 105, 106, 111], "gener": [86, 94, 103], "generate_hdf5": [18, 38, 105], "good": 85, "googl": 92, "gpu": [89, 94, 98], "guid": [86, 95], "h": 111, "help": 109, "hemi": 87, "home": 98, "how": [85, 90], "hypvinn": [9, 10, 11, 12, 62, 63, 64, 65, 66, 91, 107], "i": [85, 90], "imag": [94, 98, 107], "infer": [22, 39, 64], "input": 107, "insid": 110, "instal": [89, 110], "intel": 89, "intend": 96, "interfac": [103, 104, 105, 106, 111], "interpolation_lay": 40, "introduct": 96, "licens": 97, "linux": 89, "list": [88, 99], "load": 107, "load_config": [27, 51], "load_data": 19, "loader": [17, 36], "log": 52, "long": 109, "long_fastsurf": 109, "longitudin": 90, "loss": 41, "lr_schedul": [28, 53], "lta": 72, "maco": 89, "manual": 86, "map_surf_label": 73, "mapper": 54, "matter": 86, "measur": 111, "meter": [29, 55], "metric": [30, 56], "minimum": 96, "misc": [31, 57, 106], "model": [7, 11, 23, 24, 40, 41, 42, 43, 65, 106, 107], "modul": [83, 88, 91, 96, 110], "more": 110, "mount": 98, "multipl": [87, 110], "n4_bias_correct": 67, "name": [102, 103, 104, 105, 106, 107, 111], "nativ": [87, 89, 110], "network": [23, 42, 65, 107], "notebook": 92, "offici": [94, 98], "onli": 89, "optim": 106, "option": [88, 102, 103, 106, 107, 110, 111], "other": [88, 110], "our": 84, "output": [91, 107], "overview": [83, 86, 110], "own": 98, "packag": 89, "paint_cc_into_pr": 74, "parallel": [87, 99], "paramet": [107, 110], "parser_default": 58, "pial": 86, "pipelin": [86, 88, 99, 107, 110], "placement": 86, "pledg": 84, "polici": 93, "posit": [102, 104, 106], "possibl": 86, "practic": [94, 98], "process": [86, 87, 90, 99, 107], "proven": 94, "pull": 94, "py": [102, 103, 104, 105, 106, 107, 111], "python": 89, "question": 99, "quick": [87, 92], "quick_qc": 44, "recon": 110, "recon_surf": [67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 82], "reconstruct": 83, "reduce_to_aseg": 45, "refer": [83, 90, 96], "registr": 86, "report": [85, 93], "requir": [88, 89, 96, 107, 110], "resolut": 106, "respons": 84, "rewrite_mc_surfac": 75, "rewrite_oriented_surfac": 76, "rotate_spher": 77, "run": [87, 88, 90, 94, 100, 107], "run_model": 106, "run_predict": [25, 46, 66, 102, 103, 107], "run_tool": 59, "sample_parc": 78, "scene": 90, "scope": 84, "script": [101, 108], "secur": 93, "see": [46, 107], "segment": [83, 86, 87, 88, 91, 92], "segstat": [47, 111], "serial": 99, "set": 94, "sh": [99, 100, 109, 110], "shown": 111, "side": 86, "singl": [99, 103, 106, 110], "singular": [87, 89, 92, 98, 110], "slurm": [87, 100], "smooth_aparc": 79, "some": 88, "spherically_project_wrapp": 80, "srun_fastsurf": 100, "standard": 84, "start": 92, "statist": 90, "step": 107, "sub": 111, "sub_modul": [24, 43], "subject": [87, 99, 103, 110], "subjectx": [87, 110], "submit": 85, "subopt": 111, "suggest": 85, "support": [89, 93, 94, 98], "surf": 110, "surfac": [83, 86, 88, 91, 110], "system": [89, 96], "talairach": 86, "technic": 107, "text": 109, "thread": 60, "three": 92, "tool": 107, "train": 106, "tutori": 92, "ubuntu": 89, "us": [86, 96], "usag": [96, 98, 99, 100, 107, 109, 110], "user": [86, 95], "util": [4, 8, 12, 20, 26, 27, 28, 29, 30, 31, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 112], "version": [61, 89, 93], "via": 87, "vulner": 93, "weight": 107, "welcom": 83, "what": [86, 90], "when": [86, 88], "white": 86, "whole": 103, "window": 89, "without": 98, "wm_merge_clean": 21, "your": [90, 98]}}) \ No newline at end of file +Search.setIndex({"alltitles": {"1. Dependency packages": [[89, "dependency-packages"]], "1. System Packages": [[89, "system-packages"]], "2. Conda for python": [[89, "conda-for-python"]], "2. Python": [[89, "python"]], "3. FastSurfer": [[89, "fastsurfer"]], "3. FastSurfer and Requirements": [[89, "fastsurfer-and-requirements"]], "4. Apple AI Accelerator support": [[89, "apple-ai-accelerator-support"]], "4. Python environment": [[89, "python-environment"]], "5. FreeSurfer": [[89, "freesurfer"]], "AMD GPUs (experimental)": [[89, "amd-gpus-experimental"]], "Acknowledgements": [[83, "acknowledgements"], [96, "acknowledgements"]], "Advanced Docker Flags": [[94, "advanced-docker-flags"]], "Advanced options": [[102, "CerebNet.run_prediction-setup_options-advanced-options"], [107, "HypVINN.run_prediction-option_parse-advanced-options"]], "Advanced options (not shown in -h)": [[111, "FastSurferCNN.segstats-make_arguments-advanced-options-(not-shown-in--h)"]], "Advanced scripts": [[101, null]], "Apache License": [[97, "apache-license"]], "Attribution": [[84, "attribution"], [85, "attribution"]], "BATCH: brun_fastsurfer.sh": [[99, null]], "Before Submitting a Bug Report": [[85, "before-submitting-a-bug-report"]], "Before Submitting an Enhancement": [[85, "before-submitting-an-enhancement"]], "Behind the Scenes:": [[90, "behind-the-scenes"]], "Bias field correction": [[86, "bias-field-correction"]], "Build docker image with attestation and provenance": [[94, "build-docker-image-with-attestation-and-provenance"]], "BuildKit": [[94, "buildkit"]], "Building your own FastSurfer Singularity Image": [[98, "building-your-own-fastsurfer-singularity-image"]], "CFG-file with default options for network": [[107, "cfg-file-with-default-options-for-network"]], "CerebNet": [[0, null]], "CerebNet.apply_warp": [[13, null]], "CerebNet.data_loader.augmentation": [[14, null]], "CerebNet.data_loader.data_utils": [[15, null]], "CerebNet.data_loader.dataset": [[16, null]], "CerebNet.data_loader.loader": [[17, null]], "CerebNet.dataloader": [[1, null]], "CerebNet.datasets": [[2, null]], "CerebNet.datasets.generate_hdf5": [[18, null]], "CerebNet.datasets.load_data": [[19, null]], "CerebNet.datasets.utils": [[20, null]], "CerebNet.datasets.wm_merge_clean": [[21, null]], "CerebNet.inference": [[22, null]], "CerebNet.models.networks": [[23, null]], "CerebNet.models.sub_module": [[24, null]], "CerebNet.run_prediction": [[25, null]], "CerebNet.utils": [[4, null]], "CerebNet.utils.checkpoint": [[26, null]], "CerebNet.utils.load_config": [[27, null]], "CerebNet.utils.lr_scheduler": [[28, null]], "CerebNet.utils.meters": [[29, null]], "CerebNet.utils.metrics": [[30, null]], "CerebNet.utils.misc": [[31, null]], "CerebNet: run_prediction.py": [[102, null]], "CerebNet_models": [[3, null]], "Cerebnet module": [[91, "cerebnet-module"]], "Checkpoint to load": [[107, "checkpoint-to-load"]], "Checkpoints and configs": [[103, "checkpoints-and-configs"]], "Citation": [[107, "citation"]], "Contributing Code": [[85, "contributing-code"]], "Contributing to FastSurfer": [[85, null]], "Contributor Covenant Code of Conduct": [[84, null]], "Data options": [[106, "data-options"]], "Debugging SLURM runs": [[100, "debugging-slurm-runs"]], "Developer": [[107, "developer"]], "Docker": [[87, "docker"], [89, "docker"]], "Docker (CPU version)": [[89, "docker-cpu-version"]], "Docker (GPU version)": [[89, "docker-gpu-version"]], "Docker (currently only supported for Intel CPUs)": [[89, "docker-currently-only-supported-for-intel-cpus"]], "Docker Best Practice": [[94, "docker-best-practice"]], "Docker Flags": [[94, "docker-flags"]], "Docker Support": [[94, null]], "Dual parallel pipeline": [[99, "dual-parallel-pipeline"]], "Enforcement": [[84, "enforcement"]], "Example 1: Build GPU FastSurfer Image": [[94, "example-1-build-gpu-fastsurfer-image"]], "Example 1: FastSurfer Docker": [[87, "example-1-fastsurfer-docker"]], "Example 1: Surface module inside Docker": [[110, "example-1-surface-module-inside-docker"]], "Example 2: Build CPU FastSurfer Image": [[94, "example-2-build-cpu-fastsurfer-image"]], "Example 2: FastSurfer Singularity": [[87, "example-2-fastsurfer-singularity"]], "Example 2: recon-surf inside Singularity": [[110, "example-2-recon-surf-inside-singularity"]], "Example 3: Experimental Build for AMD GPUs": [[94, "example-3-experimental-build-for-amd-gpus"]], "Example 3: Native FastSurfer on subjectX with parallel processing of hemis": [[87, "example-3-native-fastsurfer-on-subjectx-with-parallel-processing-of-hemis"]], "Example 3: Native installation - recon-surf on a single subject (subjectX)": [[110, "example-3-native-installation-recon-surf-on-a-single-subject-subjectx"]], "Example 4: FastSurfer on multiple subjects": [[87, "example-4-fastsurfer-on-multiple-subjects"]], "Example 4: recon-surf on multiple subjects": [[110, "example-4-recon-surf-on-multiple-subjects"]], "Example 5: Quick Segmentation": [[87, "example-5-quick-segmentation"]], "Example 6: Running FastSurfer on a SLURM cluster via Singularity": [[87, "example-6-running-fastsurfer-on-a-slurm-cluster-via-singularity"]], "Example Command: Evaluation Single Subject": [[103, "example-command-evaluation-single-subject"]], "Example Command: Evaluation whole directory": [[103, "example-command-evaluation-whole-directory"]], "Example Command: Training Default FastSurferVINN": [[106, "example-command-training-default-fastsurfervinn"]], "Example Command: Training FastSurferCNN": [[106, "example-command-training-fastsurfercnn"]], "Example Command: Training FastSurferVINN (Single Resolution)": [[106, "example-command-training-fastsurfervinn-single-resolution"]], "Examples": [[87, null], [110, "examples"]], "Expert usage": [[96, "expert-usage"]], "FastSurfer API": [[81, null]], "FastSurfer Docker Image Creation": [[94, "fastsurfer-docker-image-creation"]], "FastSurfer Flags": [[87, "fastsurfer-flags"], [88, null], [94, "fastsurfer-flags"], [98, "fastsurfer-flags"]], "FastSurfer License": [[97, null]], "FastSurfer Singularity Image Usage": [[98, "fastsurfer-singularity-image-usage"]], "FastSurfer Technical parameters (see FastSurfer documentation)": [[107, "fastsurfer-technical-parameters-see-fastsurfer-documentation"]], "FastSurfer Utilities": [[112, null]], "FastSurferCNN": [[5, null]], "FastSurferCNN.data_loader": [[6, null]], "FastSurferCNN.data_loader.augmentation": [[32, null]], "FastSurferCNN.data_loader.conform": [[33, null]], "FastSurferCNN.data_loader.data_utils": [[34, null]], "FastSurferCNN.data_loader.dataset": [[35, null]], "FastSurferCNN.data_loader.loader": [[36, null]], "FastSurferCNN.download_checkpoints": [[37, null]], "FastSurferCNN.generate_hdf5": [[38, null]], "FastSurferCNN.inference": [[39, null]], "FastSurferCNN.models": [[7, null]], "FastSurferCNN.models.interpolation_layer": [[40, null]], "FastSurferCNN.models.losses": [[41, null]], "FastSurferCNN.models.networks": [[42, null]], "FastSurferCNN.models.sub_module": [[43, null]], "FastSurferCNN.quick_qc": [[44, null]], "FastSurferCNN.reduce_to_aseg": [[45, null]], "FastSurferCNN.run_prediction": [[46, null]], "FastSurferCNN.segstats": [[47, null]], "FastSurferCNN.utils": [[8, null]], "FastSurferCNN.utils.arg_types": [[48, null]], "FastSurferCNN.utils.checkpoint": [[49, null]], "FastSurferCNN.utils.common": [[50, null]], "FastSurferCNN.utils.load_config": [[51, null]], "FastSurferCNN.utils.logging": [[52, null]], "FastSurferCNN.utils.lr_scheduler": [[53, null]], "FastSurferCNN.utils.mapper": [[54, null]], "FastSurferCNN.utils.meters": [[55, null]], "FastSurferCNN.utils.metrics": [[56, null]], "FastSurferCNN.utils.misc": [[57, null]], "FastSurferCNN.utils.parser_defaults": [[58, null]], "FastSurferCNN.utils.run_tools": [[59, null]], "FastSurferCNN.utils.threads": [[60, null]], "FastSurferCNN.version": [[61, null]], "FastSurferCNN: download_checkpoints.py": [[104, null]], "FastSurferCNN: generate_hdf5.py": [[105, null]], "FastSurferCNN: run_model.py": [[106, null]], "FastSurferCNN: run_prediction.py": [[103, null]], "FastSurferCNN: segstats.py": [[111, null]], "Final Statistics:": [[90, "final-statistics"]], "Flags": [[87, "flags"]], "FreeSurfer Downstream Modules": [[96, "freesurfer-downstream-modules"]], "Full commandline interface of FastSurferCNN/download_checkpoints.py": [[104, "full-commandline-interface-of-fastsurfercnn-download-checkpoints-py"]], "Full commandline interface of FastSurferCNN/generate_hdf5.py": [[105, "full-commandline-interface-of-fastsurfercnn-generate-hdf5-py"]], "Full commandline interface of FastSurferCNN/run_model.py": [[106, "full-commandline-interface-of-fastsurfercnn-run-model-py"]], "Full commandline interface of FastSurferCNN/run_prediction.py": [[103, "full-commandline-interface-of-fastsurfercnn-run-prediction-py"]], "Full commandline interface of FastSurferCNN/segstats.py": [[111, "full-commandline-interface-of-fastsurfercnn-segstats-py"]], "Full list of flags": [[88, "full-list-of-flags"]], "General": [[103, "general"]], "General build settings": [[94, "general-build-settings"]], "General process": [[86, "general-process"]], "Google Colab": [[92, "google-colab"]], "Guide for experienced FreeSurfer users": [[86, "guide-for-experienced-freesurfer-users"]], "How Do I Submit a Good Bug Report?": [[85, "how-do-i-submit-a-good-bug-report"]], "How Do I Submit a Good Enhancement Suggestion?": [[85, "how-do-i-submit-a-good-enhancement-suggestion"]], "How to Run Your Data": [[90, "how-to-run-your-data"]], "HypVINN": [[9, null]], "HypVINN module": [[91, "hypvinn-module"]], "HypVINN.data_loader": [[10, null]], "HypVINN.data_loader.data_utils": [[62, null]], "HypVINN.data_loader.dataset": [[63, null]], "HypVINN.inference": [[64, null]], "HypVINN.models": [[11, null]], "HypVINN.models.networks": [[65, null]], "HypVINN.run_prediction": [[66, null]], "HypVINN.utils": [[12, null]], "HypVINN: run_prediction.py": [[107, null]], "Image processing options": [[107, "image-processing-options"]], "Input": [[107, "input"]], "Input and output arguments": [[107, "input-and-output-arguments"]], "Installation": [[89, null]], "Intended Use": [[96, "intended-use"]], "Introduction to FastSurfer": [[96, null]], "LONG: long_fastsurfer.sh": [[109, null]], "Linux": [[89, "linux"]], "Longitudinal Processing": [[90, null]], "MacOS": [[89, "macos"]], "Manual Edits": [[86, null]], "Minimum Requirements:": [[96, "minimum-requirements"]], "Misc. Options": [[106, "misc-options"]], "Model options": [[106, "model-options"]], "Model weights": [[107, "model-weights"]], "Mounting Home": [[98, "mounting-home"]], "Named Arguments": [[102, "CerebNet.run_prediction-setup_options-named-arguments"], [103, "FastSurferCNN.run_prediction-make_parser-named-arguments"], [104, "FastSurferCNN.download_checkpoints-make_parser-named-arguments"], [105, "FastSurferCNN.generate_hdf5-make_parser-named-arguments"], [106, "FastSurferCNN.run_model-make_parser-named-arguments"], [107, "HypVINN.run_prediction-option_parse-named-arguments"], [111, "FastSurferCNN.segstats-make_arguments-named-arguments"], [111, "named-arguments"]], "Native": [[87, "native"], [89, "native"]], "Native (Ubuntu 20.04 or Ubuntu 22.04)": [[89, "native-ubuntu-20-04-or-ubuntu-22-04"]], "Notebook 1 - Quick and Easy - FastSurfer Segmentation with three clicks": [[92, "notebook-1-quick-and-easy-fastsurfer-segmentation-with-three-clicks"]], "Notebook 2 - Complete FastSurfer Tutorial": [[92, "notebook-2-complete-fastsurfer-tutorial"]], "Optimizer options": [[106, "optimizer-options"]], "Optional commands": [[103, "optional-commands"]], "Our Pledge": [[84, "our-pledge"]], "Our Responsibilities": [[84, "our-responsibilities"]], "Our Standards": [[84, "our-standards"]], "Output": [[107, "output"]], "Output files": [[91, null]], "Overview": [[83, "overview"], [110, "overview"]], "Parallelization with brun_fastsurfer.sh": [[99, "parallelization-with-brun-fastsurfer-sh"]], "Pial surface placement": [[86, "pial-surface-placement"]], "Pipeline Steps": [[107, "pipeline-steps"]], "Pipeline overview": [[86, "pipeline-overview"]], "Positional Arguments": [[102, "CerebNet.run_prediction-setup_options-positional-arguments"], [104, "FastSurferCNN.download_checkpoints-make_parser-positional-arguments"], [106, "FastSurferCNN.run_model-make_parser-positional-arguments"]], "Possible Edits": [[86, "possible-edits"]], "Pull FastSurfer from DockerHub": [[94, "pull-fastsurfer-from-dockerhub"]], "Questions": [[99, "questions"]], "Quick Start": [[92, null]], "References": [[83, "references"], [90, "references"], [96, "references"]], "Reporting Bugs": [[85, "reporting-bugs"]], "Reporting a Vulnerability": [[93, "reporting-a-vulnerability"]], "Required arguments": [[88, "required-arguments"]], "Required for Docker when running surface module": [[88, "required-for-docker-when-running-surface-module"]], "Requirements": [[107, "requirements"]], "Running the official Docker Image": [[94, "running-the-official-docker-image"]], "Running the tool": [[107, "running-the-tool"]], "SLURM: srun_fastsurfer.sh": [[100, null]], "Scope": [[84, "scope"]], "Scripts": [[108, null]], "Security Policy": [[93, null]], "See Also": [[46, "see-also"]], "Segmentation Modules": [[83, "segmentation-modules"]], "Segmentation module": [[91, "segmentation-module"]], "Segmentation pipeline arguments (optional)": [[88, "segmentation-pipeline-arguments-optional"]], "Serial processing (default)": [[99, "serial-processing-default"]], "Side effects of edits": [[86, "side-effects-of-edits"]], "Single parallel pipeline": [[99, "single-parallel-pipeline"]], "Singularity": [[87, "singularity"], [89, "singularity"]], "Singularity Best Practice": [[98, "singularity-best-practice"]], "Singularity Flags": [[87, "singularity-flags"], [98, "singularity-flags"]], "Singularity Flags:": [[110, "singularity-flags"]], "Singularity Support": [[98, null]], "Singularity or Docker": [[92, "singularity-or-docker"]], "Singularity with the official FastSurfer Image": [[98, "singularity-with-the-official-fastsurfer-image"]], "Singularity without a GPU": [[98, "singularity-without-a-gpu"]], "Some other flags (optional)": [[88, "some-other-flags-optional"]], "Sub-commands": [[111, "Sub-commands"]], "Subject Lists": [[99, "subject-lists"]], "Suboptions": [[111, "FastSurferCNN.segstats-make_arguments-suboptions"]], "Suggesting Enhancements": [[85, "suggesting-enhancements"]], "Supported Versions": [[93, "supported-versions"]], "Surface module": [[91, "surface-module"]], "Surface pipeline arguments (optional)": [[88, "surface-pipeline-arguments-optional"]], "Surface pipeline: recon-surf.sh": [[110, null]], "Surface reconstruction": [[83, "surface-reconstruction"]], "System Requirements": [[96, "system-requirements"]], "Talairach registration": [[86, "talairach-registration"]], "Training options": [[106, "training-options"]], "Usage": [[99, "usage"], [100, "usage"], [107, "usage"], [110, "usage"]], "Usage help text": [[109, "usage-help-text"]], "User Guide": [[95, null]], "Welcome to FastSurfer!": [[83, null]], "What NOT to do": [[86, "what-not-to-do"]], "What are Edits?": [[86, "what-are-edits"]], "What can be edited?": [[86, "what-can-be-edited"]], "What is Longitudinal Processing": [[90, "what-is-longitudinal-processing"]], "What to do": [[86, "what-to-do"], [86, "id2"], [86, "id4"], [86, "id6"], [86, "id8"]], "When to use": [[86, "when-to-use"], [86, "id1"], [86, "id3"], [86, "id5"], [86, "id7"]], "White matter segmentation": [[86, "white-matter-segmentation"]], "Windows": [[89, "windows"]], "asegdkt_segfile": [[86, "asegdkt-segfile"]], "measures": [[111, "measures"]], "recon_surf": [[82, null]], "recon_surf.N4_bias_correct": [[67, null]], "recon_surf.align_points": [[68, null]], "recon_surf.align_seg": [[69, null]], "recon_surf.create_annotation": [[70, null]], "recon_surf.fs_balabels": [[71, null]], "recon_surf.lta": [[72, null]], "recon_surf.map_surf_label": [[73, null]], "recon_surf.paint_cc_into_pred": [[74, null]], "recon_surf.rewrite_mc_surface": [[75, null]], "recon_surf.rewrite_oriented_surface": [[76, null]], "recon_surf.rotate_sphere": [[77, null]], "recon_surf.sample_parc": [[78, null]], "recon_surf.smooth_aparc": [[79, null]], "recon_surf.spherically_project_wrapper": [[80, null]]}, "docnames": ["api/CerebNet", "api/CerebNet_dataloader", "api/CerebNet_datasets", "api/CerebNet_models", "api/CerebNet_utils", "api/FastSurferCNN", "api/FastSurferCNN.data_loader", "api/FastSurferCNN.models", "api/FastSurferCNN.utils", "api/HypVINN", "api/HypVINN_dataloader", "api/HypVINN_models", "api/HypVINN_utils", "api/generated/CerebNet.apply_warp", "api/generated/CerebNet.data_loader.augmentation", "api/generated/CerebNet.data_loader.data_utils", "api/generated/CerebNet.data_loader.dataset", "api/generated/CerebNet.data_loader.loader", "api/generated/CerebNet.datasets.generate_hdf5", "api/generated/CerebNet.datasets.load_data", "api/generated/CerebNet.datasets.utils", "api/generated/CerebNet.datasets.wm_merge_clean", "api/generated/CerebNet.inference", "api/generated/CerebNet.models.networks", "api/generated/CerebNet.models.sub_module", "api/generated/CerebNet.run_prediction", "api/generated/CerebNet.utils.checkpoint", "api/generated/CerebNet.utils.load_config", "api/generated/CerebNet.utils.lr_scheduler", "api/generated/CerebNet.utils.meters", "api/generated/CerebNet.utils.metrics", "api/generated/CerebNet.utils.misc", "api/generated/FastSurferCNN.data_loader.augmentation", "api/generated/FastSurferCNN.data_loader.conform", "api/generated/FastSurferCNN.data_loader.data_utils", "api/generated/FastSurferCNN.data_loader.dataset", "api/generated/FastSurferCNN.data_loader.loader", "api/generated/FastSurferCNN.download_checkpoints", "api/generated/FastSurferCNN.generate_hdf5", "api/generated/FastSurferCNN.inference", "api/generated/FastSurferCNN.models.interpolation_layer", "api/generated/FastSurferCNN.models.losses", "api/generated/FastSurferCNN.models.networks", "api/generated/FastSurferCNN.models.sub_module", "api/generated/FastSurferCNN.quick_qc", "api/generated/FastSurferCNN.reduce_to_aseg", "api/generated/FastSurferCNN.run_prediction", "api/generated/FastSurferCNN.segstats", "api/generated/FastSurferCNN.utils.arg_types", "api/generated/FastSurferCNN.utils.checkpoint", "api/generated/FastSurferCNN.utils.common", "api/generated/FastSurferCNN.utils.load_config", "api/generated/FastSurferCNN.utils.logging", "api/generated/FastSurferCNN.utils.lr_scheduler", "api/generated/FastSurferCNN.utils.mapper", "api/generated/FastSurferCNN.utils.meters", "api/generated/FastSurferCNN.utils.metrics", "api/generated/FastSurferCNN.utils.misc", "api/generated/FastSurferCNN.utils.parser_defaults", "api/generated/FastSurferCNN.utils.run_tools", "api/generated/FastSurferCNN.utils.threads", "api/generated/FastSurferCNN.version", "api/generated/HypVINN.data_loader.data_utils", "api/generated/HypVINN.data_loader.dataset", "api/generated/HypVINN.inference", "api/generated/HypVINN.models.networks", "api/generated/HypVINN.run_prediction", "api/generated/recon_surf.N4_bias_correct", "api/generated/recon_surf.align_points", "api/generated/recon_surf.align_seg", "api/generated/recon_surf.create_annotation", "api/generated/recon_surf.fs_balabels", "api/generated/recon_surf.lta", "api/generated/recon_surf.map_surf_label", "api/generated/recon_surf.paint_cc_into_pred", "api/generated/recon_surf.rewrite_mc_surface", "api/generated/recon_surf.rewrite_oriented_surface", "api/generated/recon_surf.rotate_sphere", "api/generated/recon_surf.sample_parc", "api/generated/recon_surf.smooth_aparc", "api/generated/recon_surf.spherically_project_wrapper", "api/index", "api/recon_surf", "index", "overview/CODE_OF_CONDUCT", "overview/CONTRIBUTING", "overview/EDITING", "overview/EXAMPLES", "overview/FLAGS", "overview/INSTALL", "overview/LONG", "overview/OUTPUT_FILES", "overview/QUICKSTART", "overview/SECURITY", "overview/docker", "overview/index", "overview/intro", "overview/license", "overview/singularity", "scripts/BATCH", "scripts/SLURM", "scripts/advanced", "scripts/cerebnet", "scripts/fastsurfercnn", "scripts/fastsurfercnn.download_checkpoints", "scripts/fastsurfercnn.generate_hdf5", "scripts/fastsurfercnn.run_model", "scripts/hypvinn", "scripts/index", "scripts/long_fastsurfer", "scripts/recon_surf", "scripts/segstats", "scripts/util"], "envversion": {"sphinx": 62, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinxcontrib.bibtex": 9}, "filenames": ["api/CerebNet.rst", "api/CerebNet_dataloader.rst", "api/CerebNet_datasets.rst", "api/CerebNet_models.rst", "api/CerebNet_utils.rst", "api/FastSurferCNN.rst", "api/FastSurferCNN.data_loader.rst", "api/FastSurferCNN.models.rst", "api/FastSurferCNN.utils.rst", "api/HypVINN.rst", "api/HypVINN_dataloader.rst", "api/HypVINN_models.rst", "api/HypVINN_utils.rst", "api/generated/CerebNet.apply_warp.rst", "api/generated/CerebNet.data_loader.augmentation.rst", "api/generated/CerebNet.data_loader.data_utils.rst", "api/generated/CerebNet.data_loader.dataset.rst", "api/generated/CerebNet.data_loader.loader.rst", "api/generated/CerebNet.datasets.generate_hdf5.rst", "api/generated/CerebNet.datasets.load_data.rst", "api/generated/CerebNet.datasets.utils.rst", "api/generated/CerebNet.datasets.wm_merge_clean.rst", "api/generated/CerebNet.inference.rst", "api/generated/CerebNet.models.networks.rst", "api/generated/CerebNet.models.sub_module.rst", "api/generated/CerebNet.run_prediction.rst", "api/generated/CerebNet.utils.checkpoint.rst", "api/generated/CerebNet.utils.load_config.rst", "api/generated/CerebNet.utils.lr_scheduler.rst", "api/generated/CerebNet.utils.meters.rst", "api/generated/CerebNet.utils.metrics.rst", "api/generated/CerebNet.utils.misc.rst", "api/generated/FastSurferCNN.data_loader.augmentation.rst", "api/generated/FastSurferCNN.data_loader.conform.rst", "api/generated/FastSurferCNN.data_loader.data_utils.rst", "api/generated/FastSurferCNN.data_loader.dataset.rst", "api/generated/FastSurferCNN.data_loader.loader.rst", "api/generated/FastSurferCNN.download_checkpoints.rst", "api/generated/FastSurferCNN.generate_hdf5.rst", "api/generated/FastSurferCNN.inference.rst", "api/generated/FastSurferCNN.models.interpolation_layer.rst", "api/generated/FastSurferCNN.models.losses.rst", "api/generated/FastSurferCNN.models.networks.rst", "api/generated/FastSurferCNN.models.sub_module.rst", "api/generated/FastSurferCNN.quick_qc.rst", "api/generated/FastSurferCNN.reduce_to_aseg.rst", "api/generated/FastSurferCNN.run_prediction.rst", "api/generated/FastSurferCNN.segstats.rst", "api/generated/FastSurferCNN.utils.arg_types.rst", "api/generated/FastSurferCNN.utils.checkpoint.rst", "api/generated/FastSurferCNN.utils.common.rst", "api/generated/FastSurferCNN.utils.load_config.rst", "api/generated/FastSurferCNN.utils.logging.rst", "api/generated/FastSurferCNN.utils.lr_scheduler.rst", "api/generated/FastSurferCNN.utils.mapper.rst", "api/generated/FastSurferCNN.utils.meters.rst", "api/generated/FastSurferCNN.utils.metrics.rst", "api/generated/FastSurferCNN.utils.misc.rst", "api/generated/FastSurferCNN.utils.parser_defaults.rst", "api/generated/FastSurferCNN.utils.run_tools.rst", "api/generated/FastSurferCNN.utils.threads.rst", "api/generated/FastSurferCNN.version.rst", "api/generated/HypVINN.data_loader.data_utils.rst", "api/generated/HypVINN.data_loader.dataset.rst", "api/generated/HypVINN.inference.rst", "api/generated/HypVINN.models.networks.rst", "api/generated/HypVINN.run_prediction.rst", "api/generated/recon_surf.N4_bias_correct.rst", "api/generated/recon_surf.align_points.rst", "api/generated/recon_surf.align_seg.rst", "api/generated/recon_surf.create_annotation.rst", "api/generated/recon_surf.fs_balabels.rst", "api/generated/recon_surf.lta.rst", "api/generated/recon_surf.map_surf_label.rst", "api/generated/recon_surf.paint_cc_into_pred.rst", "api/generated/recon_surf.rewrite_mc_surface.rst", "api/generated/recon_surf.rewrite_oriented_surface.rst", "api/generated/recon_surf.rotate_sphere.rst", "api/generated/recon_surf.sample_parc.rst", "api/generated/recon_surf.smooth_aparc.rst", "api/generated/recon_surf.spherically_project_wrapper.rst", "api/index.rst", "api/recon_surf.rst", "index.rst", "overview/CODE_OF_CONDUCT.md", "overview/CONTRIBUTING.md", "overview/EDITING.md", "overview/EXAMPLES.md", "overview/FLAGS.md", "overview/INSTALL.md", "overview/LONG.md", "overview/OUTPUT_FILES.md", "overview/QUICKSTART.md", "overview/SECURITY.md", "overview/docker.rst", "overview/index.rst", "overview/intro.rst", "overview/license.rst", "overview/singularity.rst", "scripts/BATCH.md", "scripts/SLURM.md", "scripts/advanced.rst", "scripts/cerebnet.rst", "scripts/fastsurfercnn.rst", "scripts/fastsurfercnn.download_checkpoints.rst", "scripts/fastsurfercnn.generate_hdf5.rst", "scripts/fastsurfercnn.run_model.rst", "scripts/hypvinn.rst", "scripts/index.rst", "scripts/long_fastsurfer.rst", "scripts/recon_surf.rst", "scripts/segstats.rst", "scripts/util.rst"], "indexentries": {"add_argument() (fastsurfercnn.utils.parser_defaults.canaddarguments method)": [[58, "FastSurferCNN.utils.parser_defaults.CanAddArguments.add_argument", false]], "add_arguments() (in module fastsurfercnn.utils.parser_defaults)": [[58, "FastSurferCNN.utils.parser_defaults.add_arguments", false]], "add_cereb_wm() (in module cerebnet.datasets.wm_merge_clean)": [[21, "CerebNet.datasets.wm_merge_clean.add_cereb_wm", false]], "add_measure_parser() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.add_measure_parser", false]], "add_plane_flags() (in module fastsurfercnn.utils.parser_defaults)": [[58, "FastSurferCNN.utils.parser_defaults.add_plane_flags", false]], "add_two_help_messages() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.add_two_help_messages", false]], "addgaussiannoise (class in fastsurfercnn.data_loader.augmentation)": [[32, "FastSurferCNN.data_loader.augmentation.AddGaussianNoise", false]], "align_aparc_centroids() (in module recon_surf.rotate_sphere)": [[77, "recon_surf.rotate_sphere.align_aparc_centroids", false]], "align_flipped() (in module recon_surf.align_seg)": [[69, "recon_surf.align_seg.align_flipped", false]], "align_seg_centroids() (in module recon_surf.align_seg)": [[69, "recon_surf.align_seg.align_seg_centroids", false]], "angles2rmat() (in module recon_surf.align_points)": [[68, "recon_surf.align_points.angles2rmat", false]], "are_all_subject_files() (fastsurfercnn.utils.common.subjectlist method)": [[50, "FastSurferCNN.utils.common.SubjectList.are_all_subject_files", false]], "args2cfg() (in module fastsurfercnn.run_prediction)": [[46, "FastSurferCNN.run_prediction.args2cfg", false]], "argument_parse() (in module recon_surf.paint_cc_into_pred)": [[74, "recon_surf.paint_cc_into_pred.argument_parse", false]], "as_future() (fastsurfercnn.utils.run_tools.popen method)": [[59, "FastSurferCNN.utils.run_tools.Popen.as_future", false]], "asegdkt_segfile (fastsurfercnn.utils.common.subjectdirectory property)": [[50, "FastSurferCNN.utils.common.SubjectDirectory.asegdkt_segfile", false]], "assert_no_root() (in module fastsurfercnn.utils.common)": [[50, "FastSurferCNN.utils.common.assert_no_root", false]], "async_save_img() (fastsurfercnn.run_prediction.runmodelondata method)": [[46, "FastSurferCNN.run_prediction.RunModelOnData.async_save_img", false]], "augmentationpadimage (class in fastsurfercnn.data_loader.augmentation)": [[32, "FastSurferCNN.data_loader.augmentation.AugmentationPadImage", false]], "augmentationrandomcrop (class in fastsurfercnn.data_loader.augmentation)": [[32, "FastSurferCNN.data_loader.augmentation.AugmentationRandomCrop", false]], "bbox_3d() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.bbox_3d", false]], "bincount2d_vectorized() (in module recon_surf.smooth_aparc)": [[79, "recon_surf.smooth_aparc.bincount2D_vectorized", false]], "borders() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.borders", false]], "bounding_volume_offset() (in module cerebnet.datasets.utils)": [[20, "CerebNet.datasets.utils.bounding_volume_offset", false]], "build_annot() (in module recon_surf.create_annotation)": [[70, "recon_surf.create_annotation.build_annot", false]], "build_model() (in module cerebnet.models.networks)": [[23, "CerebNet.models.networks.build_model", false]], "build_model() (in module fastsurfercnn.models.networks)": [[42, "FastSurferCNN.models.networks.build_model", false]], "build_model() (in module hypvinn.models.networks)": [[65, "HypVINN.models.networks.build_model", false]], "calculate_flip_orientation() (in module hypvinn.data_loader.data_utils)": [[62, "HypVINN.data_loader.data_utils.calculate_flip_orientation", false]], "calculate_merged_labels() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.calculate_merged_labels", false]], "call() (in module recon_surf.spherically_project_wrapper)": [[80, "recon_surf.spherically_project_wrapper.call", false]], "can_resolve_attribute() (fastsurfercnn.utils.common.subjectdirectory method)": [[50, "FastSurferCNN.utils.common.SubjectDirectory.can_resolve_attribute", false]], "can_resolve_filename() (fastsurfercnn.utils.common.subjectdirectory method)": [[50, "FastSurferCNN.utils.common.SubjectDirectory.can_resolve_filename", false]], "canaddarguments (class in fastsurfercnn.utils.parser_defaults)": [[58, "FastSurferCNN.utils.parser_defaults.CanAddArguments", false]], "cereb_subseg_lateral_mask() (in module cerebnet.datasets.wm_merge_clean)": [[21, "CerebNet.datasets.wm_merge_clean.cereb_subseg_lateral_mask", false]], "cerebdataset (class in cerebnet.data_loader.dataset)": [[16, "CerebNet.data_loader.dataset.CerebDataset", false]], "cerebnet.apply_warp": [[13, "module-CerebNet.apply_warp", false]], "cerebnet.data_loader.augmentation": [[14, "module-CerebNet.data_loader.augmentation", false]], "cerebnet.data_loader.data_utils": [[15, "module-CerebNet.data_loader.data_utils", false]], "cerebnet.data_loader.dataset": [[16, "module-CerebNet.data_loader.dataset", false]], "cerebnet.data_loader.loader": [[17, "module-CerebNet.data_loader.loader", false]], "cerebnet.datasets.generate_hdf5": [[18, "module-CerebNet.datasets.generate_hdf5", false]], "cerebnet.datasets.load_data": [[19, "module-CerebNet.datasets.load_data", false]], "cerebnet.datasets.utils": [[20, "module-CerebNet.datasets.utils", false]], "cerebnet.datasets.wm_merge_clean": [[21, "module-CerebNet.datasets.wm_merge_clean", false]], "cerebnet.inference": [[22, "module-CerebNet.inference", false]], "cerebnet.models.networks": [[23, "module-CerebNet.models.networks", false]], "cerebnet.models.sub_module": [[24, "module-CerebNet.models.sub_module", false]], "cerebnet.run_prediction": [[25, "module-CerebNet.run_prediction", false]], "cerebnet.utils.checkpoint": [[26, "module-CerebNet.utils.checkpoint", false]], "cerebnet.utils.load_config": [[27, "module-CerebNet.utils.load_config", false]], "cerebnet.utils.lr_scheduler": [[28, "module-CerebNet.utils.lr_scheduler", false]], "cerebnet.utils.meters": [[29, "module-CerebNet.utils.meters", false]], "cerebnet.utils.metrics": [[30, "module-CerebNet.utils.metrics", false]], "cerebnet.utils.misc": [[31, "module-CerebNet.utils.misc", false]], "cerebnetdataset (class in cerebnet.datasets.generate_hdf5)": [[18, "CerebNet.datasets.generate_hdf5.CerebNetDataset", false]], "chain() (fastsurfercnn.utils.mapper.mapper method)": [[54, "FastSurferCNN.utils.mapper.Mapper.chain", false]], "check_affine_in_nifti() (in module fastsurfercnn.data_loader.conform)": [[33, "FastSurferCNN.data_loader.conform.check_affine_in_nifti", false]], "check_and_download_ckpts() (in module fastsurfercnn.utils.checkpoint)": [[49, "FastSurferCNN.utils.checkpoint.check_and_download_ckpts", false]], "check_path() (in module fastsurfercnn.utils.misc)": [[57, "FastSurferCNN.utils.misc.check_path", false]], "check_shape_affine() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.check_shape_affine", false]], "check_volume() (in module fastsurfercnn.quick_qc)": [[44, "FastSurferCNN.quick_qc.check_volume", false]], "checkpointconfigdict (class in fastsurfercnn.utils.checkpoint)": [[49, "FastSurferCNN.utils.checkpoint.CheckpointConfigDict", false]], "classes (fastsurfercnn.utils.mapper.colorlookuptable property)": [[54, "FastSurferCNN.utils.mapper.ColorLookupTable.classes", false]], "classifierblock (class in cerebnet.models.sub_module)": [[24, "CerebNet.models.sub_module.ClassifierBlock", false]], "classifierblock (class in fastsurfercnn.models.sub_module)": [[43, "FastSurferCNN.models.sub_module.ClassifierBlock", false]], "clean_cortex_labels() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.clean_cortex_labels", false]], "color_palette (fastsurfercnn.utils.mapper.colorlookuptable property)": [[54, "FastSurferCNN.utils.mapper.ColorLookupTable.color_palette", false]], "colorlookuptable (class in fastsurfercnn.utils.mapper)": [[54, "FastSurferCNN.utils.mapper.ColorLookupTable", false]], "colormap() (fastsurfercnn.utils.mapper.colorlookuptable method)": [[54, "FastSurferCNN.utils.mapper.ColorLookupTable.colormap", false]], "combinedloss (class in fastsurfercnn.models.losses)": [[41, "FastSurferCNN.models.losses.CombinedLoss", false]], "competitivedecoderblock (class in cerebnet.models.sub_module)": [[24, "CerebNet.models.sub_module.CompetitiveDecoderBlock", false]], "competitivedecoderblock (class in fastsurfercnn.models.sub_module)": [[43, "FastSurferCNN.models.sub_module.CompetitiveDecoderBlock", false]], "competitivedenseblock (class in cerebnet.models.sub_module)": [[24, "CerebNet.models.sub_module.CompetitiveDenseBlock", false]], "competitivedenseblock (class in fastsurfercnn.models.sub_module)": [[43, "FastSurferCNN.models.sub_module.CompetitiveDenseBlock", false]], "competitivedenseblockinput (class in cerebnet.models.sub_module)": [[24, "CerebNet.models.sub_module.CompetitiveDenseBlockInput", false]], "competitivedenseblockinput (class in fastsurfercnn.models.sub_module)": [[43, "FastSurferCNN.models.sub_module.CompetitiveDenseBlockInput", false]], "competitiveencoderblock (class in cerebnet.models.sub_module)": [[24, "CerebNet.models.sub_module.CompetitiveEncoderBlock", false]], "competitiveencoderblock (class in fastsurfercnn.models.sub_module)": [[43, "FastSurferCNN.models.sub_module.CompetitiveEncoderBlock", false]], "competitiveencoderblockinput (class in cerebnet.models.sub_module)": [[24, "CerebNet.models.sub_module.CompetitiveEncoderBlockInput", false]], "competitiveencoderblockinput (class in fastsurfercnn.models.sub_module)": [[43, "FastSurferCNN.models.sub_module.CompetitiveEncoderBlockInput", false]], "comput_dice_cnf() (fastsurfercnn.utils.metrics.dicescore method)": [[56, "FastSurferCNN.utils.metrics.DiceScore.comput_dice_cnf", false]], "compute() (cerebnet.utils.metrics.dicescore method)": [[30, "CerebNet.utils.metrics.DiceScore.compute", false]], "compute_dsc() (fastsurfercnn.utils.metrics.dicescore method)": [[56, "FastSurferCNN.utils.metrics.DiceScore.compute_dsc", false]], "conf_name (fastsurfercnn.utils.common.subjectdirectory property)": [[50, "FastSurferCNN.utils.common.SubjectDirectory.conf_name", false]], "conform() (in module fastsurfercnn.data_loader.conform)": [[33, "FastSurferCNN.data_loader.conform.conform", false]], "conform_and_save_orig() (fastsurfercnn.run_prediction.runmodelondata method)": [[46, "FastSurferCNN.run_prediction.RunModelOnData.conform_and_save_orig", false]], "construct_adj_cluster() (in module recon_surf.sample_parc)": [[78, "recon_surf.sample_parc.construct_adj_cluster", false]], "copy_orig_name (fastsurfercnn.utils.common.subjectdirectory property)": [[50, "FastSurferCNN.utils.common.SubjectDirectory.copy_orig_name", false]], "correct_cereb_brainstem() (in module cerebnet.datasets.wm_merge_clean)": [[21, "CerebNet.datasets.wm_merge_clean.correct_cereb_brainstem", false]], "cortex_border_mask() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.cortex_border_mask", false]], "cosineannealingwarmrestartsdecay (class in cerebnet.utils.lr_scheduler)": [[28, "CerebNet.utils.lr_scheduler.CosineAnnealingWarmRestartsDecay", false]], "cosinelr (class in cerebnet.utils.lr_scheduler)": [[28, "CerebNet.utils.lr_scheduler.CosineLR", false]], "create_annotation() (in module recon_surf.create_annotation)": [[70, "recon_surf.create_annotation.create_annotation", false]], "create_checkpoint_dir() (in module cerebnet.utils.checkpoint)": [[26, "CerebNet.utils.checkpoint.create_checkpoint_dir", false]], "create_checkpoint_dir() (in module fastsurfercnn.utils.checkpoint)": [[49, "FastSurferCNN.utils.checkpoint.create_checkpoint_dir", false]], "create_hdf5_dataset() (cerebnet.datasets.generate_hdf5.cerebnetdataset method)": [[18, "CerebNet.datasets.generate_hdf5.CerebNetDataset.create_hdf5_dataset", false]], "create_hdf5_dataset() (fastsurfercnn.generate_hdf5.h5pydataset method)": [[38, "FastSurferCNN.generate_hdf5.H5pyDataset.create_hdf5_dataset", false]], "create_mask() (in module fastsurfercnn.reduce_to_aseg)": [[45, "FastSurferCNN.reduce_to_aseg.create_mask", false]], "create_weight_mask() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.create_weight_mask", false]], "create_weight_mask2d() (in module cerebnet.data_loader.data_utils)": [[15, "CerebNet.data_loader.data_utils.create_weight_mask2d", false]], "criteria (class in fastsurfercnn.data_loader.conform)": [[33, "FastSurferCNN.data_loader.conform.Criteria", false]], "crop_patch_to_mask() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.crop_patch_to_mask", false]], "crop_position (fastsurfercnn.models.interpolation_layer.zoom2d property)": [[40, "FastSurferCNN.models.interpolation_layer.Zoom2d.crop_position", false]], "crop_position (fastsurfercnn.models.interpolation_layer.zoom3d property)": [[40, "FastSurferCNN.models.interpolation_layer.Zoom3d.crop_position", false]], "crop_transform() (in module cerebnet.datasets.utils)": [[20, "CerebNet.datasets.utils.crop_transform", false]], "crossentropy2d (class in fastsurfercnn.models.losses)": [[41, "FastSurferCNN.models.losses.CrossEntropy2D", false]], "dataframe() (fastsurfercnn.utils.mapper.jsoncolorlookuptable method)": [[54, "FastSurferCNN.utils.mapper.JsonColorLookupTable.dataframe", false]], "dataframe() (fastsurfercnn.utils.mapper.tsvlookuptable method)": [[54, "FastSurferCNN.utils.mapper.TSVLookupTable.dataframe", false]], "decay_base_lr() (cerebnet.utils.lr_scheduler.cosineannealingwarmrestartsdecay method)": [[28, "CerebNet.utils.lr_scheduler.CosineAnnealingWarmRestartsDecay.decay_base_lr", false]], "deep_sulci_and_wm_strand_mask() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.deep_sulci_and_wm_strand_mask", false]], "dice_score() (in module cerebnet.utils.metrics)": [[30, "CerebNet.utils.metrics.dice_score", false]], "dice_score() (in module fastsurfercnn.utils.metrics)": [[56, "FastSurferCNN.utils.metrics.dice_score", false]], "diceloss (class in fastsurfercnn.models.losses)": [[41, "FastSurferCNN.models.losses.DiceLoss", false]], "dicescore (class in cerebnet.utils.metrics)": [[30, "CerebNet.utils.metrics.DiceScore", false]], "dicescore (class in fastsurfercnn.utils.metrics)": [[56, "FastSurferCNN.utils.metrics.DiceScore", false]], "disable_confusion_mat() (fastsurfercnn.utils.meters.meter method)": [[55, "FastSurferCNN.utils.meters.Meter.disable_confusion_mat", false]], "download_checkpoint() (in module fastsurfercnn.utils.checkpoint)": [[49, "FastSurferCNN.utils.checkpoint.download_checkpoint", false]], "drop_disconnected_component() (in module cerebnet.datasets.wm_merge_clean)": [[21, "CerebNet.datasets.wm_merge_clean.drop_disconnected_component", false]], "empty() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.empty", false]], "enable_confusion_mat() (fastsurfercnn.utils.meters.meter method)": [[55, "FastSurferCNN.utils.meters.Meter.enable_confusion_mat", false]], "eval() (fastsurfercnn.inference.inference method)": [[39, "FastSurferCNN.inference.Inference.eval", false]], "eval() (hypvinn.inference.inference method)": [[64, "HypVINN.inference.Inference.eval", false]], "fastsurfercnn (class in cerebnet.models.networks)": [[23, "CerebNet.models.networks.FastSurferCNN", false]], "fastsurfercnn (class in fastsurfercnn.models.networks)": [[42, "FastSurferCNN.models.networks.FastSurferCNN", false]], "fastsurfercnn.data_loader.augmentation": [[32, "module-FastSurferCNN.data_loader.augmentation", false]], "fastsurfercnn.data_loader.conform": [[33, "module-FastSurferCNN.data_loader.conform", false]], "fastsurfercnn.data_loader.data_utils": [[34, "module-FastSurferCNN.data_loader.data_utils", false]], "fastsurfercnn.data_loader.dataset": [[35, "module-FastSurferCNN.data_loader.dataset", false]], "fastsurfercnn.data_loader.loader": [[36, "module-FastSurferCNN.data_loader.loader", false]], "fastsurfercnn.download_checkpoints": [[37, "module-FastSurferCNN.download_checkpoints", false]], "fastsurfercnn.generate_hdf5": [[38, "module-FastSurferCNN.generate_hdf5", false]], "fastsurfercnn.inference": [[39, "module-FastSurferCNN.inference", false]], "fastsurfercnn.models.interpolation_layer": [[40, "module-FastSurferCNN.models.interpolation_layer", false]], "fastsurfercnn.models.losses": [[41, "module-FastSurferCNN.models.losses", false]], "fastsurfercnn.models.networks": [[42, "module-FastSurferCNN.models.networks", false]], "fastsurfercnn.models.sub_module": [[43, "module-FastSurferCNN.models.sub_module", false]], "fastsurfercnn.quick_qc": [[44, "module-FastSurferCNN.quick_qc", false]], "fastsurfercnn.reduce_to_aseg": [[45, "module-FastSurferCNN.reduce_to_aseg", false]], "fastsurfercnn.run_prediction": [[46, "module-FastSurferCNN.run_prediction", false]], "fastsurfercnn.segstats": [[47, "module-FastSurferCNN.segstats", false]], "fastsurfercnn.utils.arg_types": [[48, "module-FastSurferCNN.utils.arg_types", false]], "fastsurfercnn.utils.checkpoint": [[49, "module-FastSurferCNN.utils.checkpoint", false]], "fastsurfercnn.utils.common": [[50, "module-FastSurferCNN.utils.common", false]], "fastsurfercnn.utils.load_config": [[51, "module-FastSurferCNN.utils.load_config", false]], "fastsurfercnn.utils.logging": [[52, "module-FastSurferCNN.utils.logging", false]], "fastsurfercnn.utils.lr_scheduler": [[53, "module-FastSurferCNN.utils.lr_scheduler", false]], "fastsurfercnn.utils.mapper": [[54, "module-FastSurferCNN.utils.mapper", false]], "fastsurfercnn.utils.meters": [[55, "module-FastSurferCNN.utils.meters", false]], "fastsurfercnn.utils.metrics": [[56, "module-FastSurferCNN.utils.metrics", false]], "fastsurfercnn.utils.misc": [[57, "module-FastSurferCNN.utils.misc", false]], "fastsurfercnn.utils.parser_defaults": [[58, "module-FastSurferCNN.utils.parser_defaults", false]], "fastsurfercnn.utils.run_tools": [[59, "module-FastSurferCNN.utils.run_tools", false]], "fastsurfercnn.utils.threads": [[60, "module-FastSurferCNN.utils.threads", false]], "fastsurfercnn.version": [[61, "module-FastSurferCNN.version", false]], "fastsurfercnnbase (class in fastsurfercnn.models.networks)": [[42, "FastSurferCNN.models.networks.FastSurferCNNBase", false]], "fastsurfervinn (class in fastsurfercnn.models.networks)": [[42, "FastSurferCNN.models.networks.FastSurferVINN", false]], "fileexists_by_attribute() (fastsurfercnn.utils.common.subjectdirectory method)": [[50, "FastSurferCNN.utils.common.SubjectDirectory.fileexists_by_attribute", false]], "fileexists_in_subject_folder() (fastsurfercnn.utils.common.subjectdirectory method)": [[50, "FastSurferCNN.utils.common.SubjectDirectory.fileexists_in_subject_folder", false]], "filename_by_attribute() (fastsurfercnn.utils.common.subjectdirectory method)": [[50, "FastSurferCNN.utils.common.SubjectDirectory.filename_by_attribute", false]], "filename_in_subject_folder() (fastsurfercnn.utils.common.subjectdirectory method)": [[50, "FastSurferCNN.utils.common.SubjectDirectory.filename_in_subject_folder", false]], "fill_unknown_labels_per_hemi() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.fill_unknown_labels_per_hemi", false]], "filling_unknown_labels() (in module cerebnet.datasets.wm_merge_clean)": [[21, "CerebNet.datasets.wm_merge_clean.filling_unknown_labels", false]], "filter_blank_slices_thick() (in module cerebnet.data_loader.data_utils)": [[15, "CerebNet.data_loader.data_utils.filter_blank_slices_thick", false]], "filter_blank_slices_thick() (in module cerebnet.datasets.utils)": [[20, "CerebNet.datasets.utils.filter_blank_slices_thick", false]], "filter_blank_slices_thick() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.filter_blank_slices_thick", false]], "filter_git_status() (in module fastsurfercnn.version)": [[61, "FastSurferCNN.version.filter_git_status", false]], "find_affine() (in module recon_surf.align_points)": [[68, "recon_surf.align_points.find_affine", false]], "find_all_islands() (in module recon_surf.sample_parc)": [[78, "recon_surf.sample_parc.find_all_islands", false]], "find_device() (in module fastsurfercnn.utils.common)": [[50, "FastSurferCNN.utils.common.find_device", false]], "find_img_size_by_fov() (in module fastsurfercnn.data_loader.conform)": [[33, "FastSurferCNN.data_loader.conform.find_img_size_by_fov", false]], "find_latest_experiment() (in module fastsurfercnn.utils.misc)": [[57, "FastSurferCNN.utils.misc.find_latest_experiment", false]], "find_min_size() (in module fastsurfercnn.data_loader.conform)": [[33, "FastSurferCNN.data_loader.conform.find_min_size", false]], "find_rigid() (in module recon_surf.align_points)": [[68, "recon_surf.align_points.find_rigid", false]], "find_rotation() (in module recon_surf.align_points)": [[68, "recon_surf.align_points.find_rotation", false]], "finish() (fastsurfercnn.utils.run_tools.popen method)": [[59, "FastSurferCNN.utils.run_tools.Popen.finish", false]], "flags (fastsurfercnn.utils.common.subjectlist property)": [[50, "FastSurferCNN.utils.common.SubjectList.flags", false]], "flip_wm_islands() (in module fastsurfercnn.reduce_to_aseg)": [[45, "FastSurferCNN.reduce_to_aseg.flip_wm_islands", false]], "float_gt_zero_and_le_one() (in module fastsurfercnn.utils.arg_types)": [[48, "FastSurferCNN.utils.arg_types.float_gt_zero_and_le_one", false]], "format_parameters() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.format_parameters", false]], "forward() (cerebnet.models.networks.fastsurfercnn method)": [[23, "CerebNet.models.networks.FastSurferCNN.forward", false]], "forward() (cerebnet.models.sub_module.classifierblock method)": [[24, "CerebNet.models.sub_module.ClassifierBlock.forward", false]], "forward() (cerebnet.models.sub_module.competitivedecoderblock method)": [[24, "CerebNet.models.sub_module.CompetitiveDecoderBlock.forward", false]], "forward() (cerebnet.models.sub_module.competitivedenseblock method)": [[24, "CerebNet.models.sub_module.CompetitiveDenseBlock.forward", false]], "forward() (cerebnet.models.sub_module.competitivedenseblockinput method)": [[24, "CerebNet.models.sub_module.CompetitiveDenseBlockInput.forward", false]], "forward() (cerebnet.models.sub_module.competitiveencoderblock method)": [[24, "CerebNet.models.sub_module.CompetitiveEncoderBlock.forward", false]], "forward() (cerebnet.models.sub_module.competitiveencoderblockinput method)": [[24, "CerebNet.models.sub_module.CompetitiveEncoderBlockInput.forward", false]], "forward() (fastsurfercnn.models.losses.combinedloss method)": [[41, "FastSurferCNN.models.losses.CombinedLoss.forward", false]], "forward() (fastsurfercnn.models.losses.crossentropy2d method)": [[41, "FastSurferCNN.models.losses.CrossEntropy2D.forward", false]], "forward() (fastsurfercnn.models.losses.diceloss method)": [[41, "FastSurferCNN.models.losses.DiceLoss.forward", false]], "forward() (fastsurfercnn.models.networks.fastsurfercnn method)": [[42, "FastSurferCNN.models.networks.FastSurferCNN.forward", false]], "forward() (fastsurfercnn.models.networks.fastsurfercnnbase method)": [[42, "FastSurferCNN.models.networks.FastSurferCNNBase.forward", false]], "forward() (fastsurfercnn.models.networks.fastsurfervinn method)": [[42, "FastSurferCNN.models.networks.FastSurferVINN.forward", false]], "forward() (fastsurfercnn.models.sub_module.classifierblock method)": [[43, "FastSurferCNN.models.sub_module.ClassifierBlock.forward", false]], "forward() (fastsurfercnn.models.sub_module.competitivedecoderblock method)": [[43, "FastSurferCNN.models.sub_module.CompetitiveDecoderBlock.forward", false]], "forward() (fastsurfercnn.models.sub_module.competitivedenseblock method)": [[43, "FastSurferCNN.models.sub_module.CompetitiveDenseBlock.forward", false]], "forward() (fastsurfercnn.models.sub_module.competitivedenseblockinput method)": [[43, "FastSurferCNN.models.sub_module.CompetitiveDenseBlockInput.forward", false]], "forward() (fastsurfercnn.models.sub_module.competitiveencoderblock method)": [[43, "FastSurferCNN.models.sub_module.CompetitiveEncoderBlock.forward", false]], "forward() (fastsurfercnn.models.sub_module.competitiveencoderblockinput method)": [[43, "FastSurferCNN.models.sub_module.CompetitiveEncoderBlockInput.forward", false]], "forward() (fastsurfercnn.models.sub_module.gaussiannoise method)": [[43, "FastSurferCNN.models.sub_module.GaussianNoise.forward", false]], "forward() (fastsurfercnn.models.sub_module.inputdenseblock method)": [[43, "FastSurferCNN.models.sub_module.InputDenseBlock.forward", false]], "forward() (fastsurfercnn.models.sub_module.outputdenseblock method)": [[43, "FastSurferCNN.models.sub_module.OutputDenseBlock.forward", false]], "forward() (hypvinn.models.networks.hypvinn method)": [[65, "HypVINN.models.networks.HypVINN.forward", false]], "fuse_cortex_labels() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.fuse_cortex_labels", false]], "gaussiannoise (class in fastsurfercnn.models.sub_module)": [[43, "FastSurferCNN.models.sub_module.GaussianNoise", false]], "get_adjm() (in module recon_surf.smooth_aparc)": [[79, "recon_surf.smooth_aparc.get_adjM", false]], "get_aseg_cereb_mask() (in module cerebnet.data_loader.data_utils)": [[15, "CerebNet.data_loader.data_utils.get_aseg_cereb_mask", false]], "get_attribute() (fastsurfercnn.utils.common.subjectdirectory method)": [[50, "FastSurferCNN.utils.common.SubjectDirectory.get_attribute", false]], "get_brain_centroid() (in module recon_surf.n4_bias_correct)": [[67, "recon_surf.N4_bias_correct.get_brain_centroid", false]], "get_cfg() (fastsurfercnn.inference.inference method)": [[39, "FastSurferCNN.inference.Inference.get_cfg", false]], "get_cfg() (hypvinn.inference.inference method)": [[64, "HypVINN.inference.Inference.get_cfg", false]], "get_checkpoint() (in module cerebnet.utils.checkpoint)": [[26, "CerebNet.utils.checkpoint.get_checkpoint", false]], "get_checkpoint() (in module fastsurfercnn.utils.checkpoint)": [[49, "FastSurferCNN.utils.checkpoint.get_checkpoint", false]], "get_checkpoint_path() (in module cerebnet.utils.checkpoint)": [[26, "CerebNet.utils.checkpoint.get_checkpoint_path", false]], "get_checkpoint_path() (in module fastsurfercnn.utils.checkpoint)": [[49, "FastSurferCNN.utils.checkpoint.get_checkpoint_path", false]], "get_checkpoints() (in module fastsurfercnn.utils.checkpoint)": [[49, "FastSurferCNN.utils.checkpoint.get_checkpoints", false]], "get_color_by_index() (fastsurfercnn.utils.mapper.colorlookuptable method)": [[54, "FastSurferCNN.utils.mapper.ColorLookupTable.get_color_by_index", false]], "get_common_suffix() (fastsurfercnn.utils.common.subjectlist method)": [[50, "FastSurferCNN.utils.common.SubjectList.get_common_suffix", false]], "get_config() (in module cerebnet.utils.load_config)": [[27, "CerebNet.utils.load_config.get_config", false]], "get_config() (in module fastsurfercnn.utils.load_config)": [[51, "FastSurferCNN.utils.load_config.get_config", false]], "get_conformed_vox_img_size() (in module fastsurfercnn.data_loader.conform)": [[33, "FastSurferCNN.data_loader.conform.get_conformed_vox_img_size", false]], "get_dataloader() (in module cerebnet.data_loader.loader)": [[17, "CerebNet.data_loader.loader.get_dataloader", false]], "get_dataloader() (in module fastsurfercnn.data_loader.loader)": [[36, "FastSurferCNN.data_loader.loader.get_dataloader", false]], "get_default_version_info() (in module fastsurfercnn.version)": [[61, "FastSurferCNN.version.get_default_version_info", false]], "get_device() (fastsurfercnn.inference.inference method)": [[39, "FastSurferCNN.inference.Inference.get_device", false]], "get_device() (hypvinn.inference.inference method)": [[64, "HypVINN.inference.Inference.get_device", false]], "get_epoch_lr() (cerebnet.utils.lr_scheduler.cosinelr method)": [[28, "CerebNet.utils.lr_scheduler.CosineLR.get_epoch_lr", false]], "get_image_mean() (in module recon_surf.n4_bias_correct)": [[67, "recon_surf.N4_bias_correct.get_image_mean", false]], "get_labels_from_lut() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.get_labels_from_lut", false]], "get_largest_cc() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.get_largest_cc", false]], "get_loss_func() (in module fastsurfercnn.models.losses)": [[41, "FastSurferCNN.models.losses.get_loss_func", false]], "get_lr() (cerebnet.utils.lr_scheduler.warmupcosinelr method)": [[28, "CerebNet.utils.lr_scheduler.WarmupCosineLR.get_lr", false]], "get_lr_scheduler() (in module cerebnet.utils.lr_scheduler)": [[28, "CerebNet.utils.lr_scheduler.get_lr_scheduler", false]], "get_lr_scheduler() (in module fastsurfercnn.utils.lr_scheduler)": [[53, "FastSurferCNN.utils.lr_scheduler.get_lr_scheduler", false]], "get_max_size() (fastsurfercnn.inference.inference method)": [[39, "FastSurferCNN.inference.Inference.get_max_size", false]], "get_max_size() (hypvinn.inference.inference method)": [[64, "HypVINN.inference.Inference.get_max_size", false]], "get_model_height() (fastsurfercnn.inference.inference method)": [[39, "FastSurferCNN.inference.Inference.get_model_height", false]], "get_model_height() (hypvinn.inference.inference method)": [[64, "HypVINN.inference.Inference.get_model_height", false]], "get_model_width() (fastsurfercnn.inference.inference method)": [[39, "FastSurferCNN.inference.Inference.get_model_width", false]], "get_model_width() (hypvinn.inference.inference method)": [[64, "HypVINN.inference.Inference.get_model_width", false]], "get_modelname() (fastsurfercnn.inference.inference method)": [[39, "FastSurferCNN.inference.Inference.get_modelname", false]], "get_modelname() (hypvinn.inference.inference method)": [[64, "HypVINN.inference.Inference.get_modelname", false]], "get_num_classes() (fastsurfercnn.inference.inference method)": [[39, "FastSurferCNN.inference.Inference.get_num_classes", false]], "get_num_classes() (fastsurfercnn.run_prediction.runmodelondata method)": [[46, "FastSurferCNN.run_prediction.RunModelOnData.get_num_classes", false]], "get_num_classes() (hypvinn.inference.inference method)": [[64, "HypVINN.inference.Inference.get_num_classes", false]], "get_num_threads() (in module fastsurfercnn.utils.threads)": [[60, "FastSurferCNN.utils.threads.get_num_threads", false]], "get_plane() (fastsurfercnn.inference.inference method)": [[39, "FastSurferCNN.inference.Inference.get_plane", false]], "get_plane() (hypvinn.inference.inference method)": [[64, "HypVINN.inference.Inference.get_plane", false]], "get_prediction() (fastsurfercnn.run_prediction.runmodelondata method)": [[46, "FastSurferCNN.run_prediction.RunModelOnData.get_prediction", false]], "get_prediction() (in module hypvinn.run_prediction)": [[66, "HypVINN.run_prediction.get_prediction", false]], "get_region_bg_intersection_mask() (in module fastsurfercnn.quick_qc)": [[44, "FastSurferCNN.quick_qc.get_region_bg_intersection_mask", false]], "get_seg_centroids() (in module recon_surf.align_seg)": [[69, "recon_surf.align_seg.get_seg_centroids", false]], "get_subject_names() (fastsurfercnn.data_loader.dataset.multiscaledataset method)": [[35, "FastSurferCNN.data_loader.dataset.MultiScaleDataset.get_subject_names", false]], "get_subject_names() (fastsurfercnn.data_loader.dataset.multiscaledatasetval method)": [[35, "FastSurferCNN.data_loader.dataset.MultiScaleDatasetVal.get_subject_names", false]], "get_tal_origin_voxel() (in module recon_surf.n4_bias_correct)": [[67, "recon_surf.N4_bias_correct.get_tal_origin_voxel", false]], "get_thick_slices() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.get_thick_slices", false]], "get_ventricle_bg_intersection_volume() (in module fastsurfercnn.quick_qc)": [[44, "FastSurferCNN.quick_qc.get_ventricle_bg_intersection_volume", false]], "get_vox2ras() (in module recon_surf.align_seg)": [[69, "recon_surf.align_seg.get_vox2ras", false]], "getitem_by_index() (fastsurfercnn.utils.mapper.colorlookuptable method)": [[54, "FastSurferCNN.utils.mapper.ColorLookupTable.getitem_by_index", false]], "getitem_by_index() (fastsurfercnn.utils.mapper.tsvlookuptable method)": [[54, "FastSurferCNN.utils.mapper.TSVLookupTable.getitem_by_index", false]], "getscale() (in module fastsurfercnn.data_loader.conform)": [[33, "FastSurferCNN.data_loader.conform.getscale", false]], "getsurfcorrespondence() (in module recon_surf.map_surf_label)": [[73, "recon_surf.map_surf_label.getSurfCorrespondence", false]], "global_stats() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.global_stats", false]], "h5pydataset (class in fastsurfercnn.generate_hdf5)": [[38, "FastSurferCNN.generate_hdf5.H5pyDataset", false]], "handle_cuda_memory_exception() (in module fastsurfercnn.utils.common)": [[50, "FastSurferCNN.utils.common.handle_cuda_memory_exception", false]], "has_attribute() (fastsurfercnn.utils.common.subjectdirectory method)": [[50, "FastSurferCNN.utils.common.SubjectDirectory.has_attribute", false]], "has_git() (in module fastsurfercnn.version)": [[61, "FastSurferCNN.version.has_git", false]], "hd() (in module cerebnet.utils.metrics)": [[30, "CerebNet.utils.metrics.hd", false]], "hd95() (in module cerebnet.utils.metrics)": [[30, "CerebNet.utils.metrics.hd95", false]], "helpformatter (class in fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.HelpFormatter", false]], "hypo_map_label2subseg() (in module hypvinn.data_loader.data_utils)": [[62, "HypVINN.data_loader.data_utils.hypo_map_label2subseg", false]], "hypo_map_prediction_sagittal2full() (in module hypvinn.data_loader.data_utils)": [[62, "HypVINN.data_loader.data_utils.hypo_map_prediction_sagittal2full", false]], "hypo_map_subseg_2_fsseg() (in module hypvinn.data_loader.data_utils)": [[62, "HypVINN.data_loader.data_utils.hypo_map_subseg_2_fsseg", false]], "hypvinn (class in hypvinn.models.networks)": [[65, "HypVINN.models.networks.HypVINN", false]], "hypvinn.data_loader.data_utils": [[62, "module-HypVINN.data_loader.data_utils", false]], "hypvinn.data_loader.dataset": [[63, "module-HypVINN.data_loader.dataset", false]], "hypvinn.inference": [[64, "module-HypVINN.inference", false]], "hypvinn.models.networks": [[65, "module-HypVINN.models.networks", false]], "hypvinn.run_prediction": [[66, "module-HypVINN.run_prediction", false]], "hypvinndataset (class in hypvinn.data_loader.dataset)": [[63, "HypVINN.data_loader.dataset.HypVINNDataset", false]], "id (fastsurfercnn.utils.common.subjectdirectory property)": [[50, "FastSurferCNN.utils.common.SubjectDirectory.id", false]], "infer_labels_excludeid() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.infer_labels_excludeid", false]], "infer_mapping_from_lut() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.infer_mapping_from_lut", false]], "infer_merged_labels() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.infer_merged_labels", false]], "inference (class in cerebnet.inference)": [[22, "CerebNet.inference.Inference", false]], "inference (class in fastsurfercnn.inference)": [[39, "FastSurferCNN.inference.Inference", false]], "inference (class in hypvinn.inference)": [[64, "HypVINN.inference.Inference", false]], "inputdenseblock (class in fastsurfercnn.models.sub_module)": [[43, "FastSurferCNN.models.sub_module.InputDenseBlock", false]], "int_ge_zero() (in module fastsurfercnn.utils.arg_types)": [[48, "FastSurferCNN.utils.arg_types.int_ge_zero", false]], "int_gt_zero() (in module fastsurfercnn.utils.arg_types)": [[48, "FastSurferCNN.utils.arg_types.int_gt_zero", false]], "iou_score() (in module fastsurfercnn.utils.metrics)": [[56, "FastSurferCNN.utils.metrics.iou_score", false]], "is_bijective() (fastsurfercnn.utils.mapper.mapper method)": [[54, "FastSurferCNN.utils.mapper.Mapper.is_bijective", false]], "is_checkpoint_epoch() (in module cerebnet.utils.checkpoint)": [[26, "CerebNet.utils.checkpoint.is_checkpoint_epoch", false]], "is_conform() (in module fastsurfercnn.data_loader.conform)": [[33, "FastSurferCNN.data_loader.conform.is_conform", false]], "is_int() (in module fastsurfercnn.utils.mapper)": [[54, "FastSurferCNN.utils.mapper.is_int", false]], "is_lia() (in module fastsurfercnn.data_loader.conform)": [[33, "FastSurferCNN.data_loader.conform.is_lia", false]], "is_resampling_vox2vox() (in module fastsurfercnn.data_loader.conform)": [[33, "FastSurferCNN.data_loader.conform.is_resampling_vox2vox", false]], "iterate() (in module fastsurfercnn.utils.common)": [[50, "FastSurferCNN.utils.common.iterate", false]], "itk_n4_bfcorrection() (in module recon_surf.n4_bias_correct)": [[67, "recon_surf.N4_bias_correct.itk_n4_bfcorrection", false]], "jsoncolorlookuptable (class in fastsurfercnn.utils.mapper)": [[54, "FastSurferCNN.utils.mapper.JsonColorLookupTable", false]], "labelname2id() (fastsurfercnn.utils.mapper.colorlookuptable method)": [[54, "FastSurferCNN.utils.mapper.ColorLookupTable.labelname2id", false]], "labelname2id() (fastsurfercnn.utils.mapper.jsoncolorlookuptable method)": [[54, "FastSurferCNN.utils.mapper.JsonColorLookupTable.labelname2id", false]], "labelname2id() (fastsurfercnn.utils.mapper.tsvlookuptable method)": [[54, "FastSurferCNN.utils.mapper.TSVLookupTable.labelname2id", false]], "labelname2index() (fastsurfercnn.utils.mapper.colorlookuptable method)": [[54, "FastSurferCNN.utils.mapper.ColorLookupTable.labelname2index", false]], "load_and_conform_image() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.load_and_conform_image", false]], "load_checkpoint() (fastsurfercnn.inference.inference method)": [[39, "FastSurferCNN.inference.Inference.load_checkpoint", false]], "load_checkpoint() (hypvinn.inference.inference method)": [[64, "HypVINN.inference.Inference.load_checkpoint", false]], "load_checkpoint_config() (in module fastsurfercnn.utils.checkpoint)": [[49, "FastSurferCNN.utils.checkpoint.load_checkpoint_config", false]], "load_checkpoint_config_defaults() (in module fastsurfercnn.utils.checkpoint)": [[49, "FastSurferCNN.utils.checkpoint.load_checkpoint_config_defaults", false]], "load_classwise_weights() (in module cerebnet.utils.misc)": [[31, "CerebNet.utils.misc.load_classwise_weights", false]], "load_config() (in module fastsurfercnn.utils.load_config)": [[51, "FastSurferCNN.utils.load_config.load_config", false]], "load_from_checkpoint() (in module cerebnet.utils.checkpoint)": [[26, "CerebNet.utils.checkpoint.load_from_checkpoint", false]], "load_from_checkpoint() (in module fastsurfercnn.utils.checkpoint)": [[49, "FastSurferCNN.utils.checkpoint.load_from_checkpoint", false]], "load_image() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.load_image", false]], "load_maybe_conform() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.load_maybe_conform", false]], "load_subject() (cerebnet.datasets.load_data.subjectloader method)": [[19, "CerebNet.datasets.load_data.SubjectLoader.load_subject", false]], "load_test_subject() (cerebnet.datasets.load_data.subjectloader method)": [[19, "CerebNet.datasets.load_data.SubjectLoader.load_test_subject", false]], "load_volumes() (in module hypvinn.run_prediction)": [[66, "HypVINN.run_prediction.load_volumes", false]], "locate_mask_bbox() (cerebnet.data_loader.dataset.subjectdataset method)": [[16, "CerebNet.data_loader.dataset.SubjectDataset.locate_mask_bbox", false]], "locating_unknowns() (in module cerebnet.datasets.wm_merge_clean)": [[21, "CerebNet.datasets.wm_merge_clean.locating_unknowns", false]], "log_epoch() (cerebnet.utils.meters.meter method)": [[29, "CerebNet.utils.meters.Meter.log_epoch", false]], "log_epoch() (fastsurfercnn.utils.meters.meter method)": [[55, "FastSurferCNN.utils.meters.Meter.log_epoch", false]], "log_iter() (cerebnet.utils.meters.meter method)": [[29, "CerebNet.utils.meters.Meter.log_iter", false]], "log_iter() (fastsurfercnn.utils.meters.meter method)": [[55, "FastSurferCNN.utils.meters.Meter.log_iter", false]], "log_lr() (cerebnet.utils.meters.meter method)": [[29, "CerebNet.utils.meters.Meter.log_lr", false]], "lr_func_cosine() (cerebnet.utils.lr_scheduler.cosinelr method)": [[28, "CerebNet.utils.lr_scheduler.CosineLR.lr_func_cosine", false]], "ltadict (class in cerebnet.datasets.utils)": [[20, "CerebNet.datasets.utils.LTADict", false]], "main() (in module cerebnet.apply_warp)": [[13, "CerebNet.apply_warp.main", false]], "main() (in module cerebnet.run_prediction)": [[25, "CerebNet.run_prediction.main", false]], "main() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.main", false]], "main() (in module fastsurfercnn.version)": [[61, "FastSurferCNN.version.main", false]], "main() (in module hypvinn.run_prediction)": [[66, "HypVINN.run_prediction.main", false]], "main() (in module recon_surf.smooth_aparc)": [[79, "recon_surf.smooth_aparc.main", false]], "main_segfile (fastsurfercnn.utils.common.subjectdirectory property)": [[50, "FastSurferCNN.utils.common.SubjectDirectory.main_segfile", false]], "make_arguments() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.make_arguments", false]], "make_classmapper() (fastsurfercnn.utils.mapper.mapper class method)": [[54, "FastSurferCNN.utils.mapper.Mapper.make_classmapper", false]], "make_parser() (in module fastsurfercnn.data_loader.conform)": [[33, "FastSurferCNN.data_loader.conform.make_parser", false]], "make_parser() (in module fastsurfercnn.run_prediction)": [[46, "FastSurferCNN.run_prediction.make_parser", false]], "make_parser() (in module fastsurfercnn.version)": [[61, "FastSurferCNN.version.make_parser", false]], "make_parser() (in module recon_surf.rewrite_oriented_surface)": [[76, "recon_surf.rewrite_oriented_surface.make_parser", false]], "make_subjects_dir() (fastsurfercnn.utils.common.subjectlist method)": [[50, "FastSurferCNN.utils.common.SubjectList.make_subjects_dir", false]], "map() (fastsurfercnn.utils.common.serialexecutor method)": [[50, "FastSurferCNN.utils.common.SerialExecutor.map", false]], "map() (fastsurfercnn.utils.mapper.mapper method)": [[54, "FastSurferCNN.utils.mapper.Mapper.map", false]], "map_aparc_aseg2label() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.map_aparc_aseg2label", false]], "map_image() (in module fastsurfercnn.data_loader.conform)": [[33, "FastSurferCNN.data_loader.conform.map_image", false]], "map_label2aparc_aseg() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.map_label2aparc_aseg", false]], "map_label2subseg() (in module cerebnet.datasets.utils)": [[20, "CerebNet.datasets.utils.map_label2subseg", false]], "map_multiple_labels() (in module recon_surf.create_annotation)": [[70, "recon_surf.create_annotation.map_multiple_labels", false]], "map_prediction_sagittal2full() (in module cerebnet.data_loader.data_utils)": [[15, "CerebNet.data_loader.data_utils.map_prediction_sagittal2full", false]], "map_prediction_sagittal2full() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.map_prediction_sagittal2full", false]], "map_sag2label() (in module cerebnet.data_loader.data_utils)": [[15, "CerebNet.data_loader.data_utils.map_sag2label", false]], "map_size() (in module cerebnet.datasets.utils)": [[20, "CerebNet.datasets.utils.map_size", false]], "mapper (class in fastsurfercnn.utils.mapper)": [[54, "FastSurferCNN.utils.mapper.Mapper", false]], "mapsurflabel() (in module recon_surf.map_surf_label)": [[73, "recon_surf.map_surf_label.mapSurfLabel", false]], "max_label (fastsurfercnn.utils.mapper.mapper property)": [[54, "FastSurferCNN.utils.mapper.Mapper.max_label", false]], "messagebuffer (class in fastsurfercnn.utils.run_tools)": [[59, "FastSurferCNN.utils.run_tools.MessageBuffer", false]], "meter (class in cerebnet.utils.meters)": [[29, "CerebNet.utils.meters.Meter", false]], "meter (class in fastsurfercnn.utils.meters)": [[55, "FastSurferCNN.utils.meters.Meter", false]], "metrics_per_class() (cerebnet.utils.meters.testmeter method)": [[29, "CerebNet.utils.meters.TestMeter.metrics_per_class", false]], "mode_filter() (in module recon_surf.smooth_aparc)": [[79, "recon_surf.smooth_aparc.mode_filter", false]], "module": [[13, "module-CerebNet.apply_warp", false], [14, "module-CerebNet.data_loader.augmentation", false], [15, "module-CerebNet.data_loader.data_utils", false], [16, "module-CerebNet.data_loader.dataset", false], [17, "module-CerebNet.data_loader.loader", false], [18, "module-CerebNet.datasets.generate_hdf5", false], [19, "module-CerebNet.datasets.load_data", false], [20, "module-CerebNet.datasets.utils", false], [21, "module-CerebNet.datasets.wm_merge_clean", false], [22, "module-CerebNet.inference", false], [23, "module-CerebNet.models.networks", false], [24, "module-CerebNet.models.sub_module", false], [25, "module-CerebNet.run_prediction", false], [26, "module-CerebNet.utils.checkpoint", false], [27, "module-CerebNet.utils.load_config", false], [28, "module-CerebNet.utils.lr_scheduler", false], [29, "module-CerebNet.utils.meters", false], [30, "module-CerebNet.utils.metrics", false], [31, "module-CerebNet.utils.misc", false], [32, "module-FastSurferCNN.data_loader.augmentation", false], [33, "module-FastSurferCNN.data_loader.conform", false], [34, "module-FastSurferCNN.data_loader.data_utils", false], [35, "module-FastSurferCNN.data_loader.dataset", false], [36, "module-FastSurferCNN.data_loader.loader", false], [37, "module-FastSurferCNN.download_checkpoints", false], [38, "module-FastSurferCNN.generate_hdf5", false], [39, "module-FastSurferCNN.inference", false], [40, "module-FastSurferCNN.models.interpolation_layer", false], [41, "module-FastSurferCNN.models.losses", false], [42, "module-FastSurferCNN.models.networks", false], [43, "module-FastSurferCNN.models.sub_module", false], [44, "module-FastSurferCNN.quick_qc", false], [45, "module-FastSurferCNN.reduce_to_aseg", false], [46, "module-FastSurferCNN.run_prediction", false], [47, "module-FastSurferCNN.segstats", false], [48, "module-FastSurferCNN.utils.arg_types", false], [49, "module-FastSurferCNN.utils.checkpoint", false], [50, "module-FastSurferCNN.utils.common", false], [51, "module-FastSurferCNN.utils.load_config", false], [52, "module-FastSurferCNN.utils.logging", false], [53, "module-FastSurferCNN.utils.lr_scheduler", false], [54, "module-FastSurferCNN.utils.mapper", false], [55, "module-FastSurferCNN.utils.meters", false], [56, "module-FastSurferCNN.utils.metrics", false], [57, "module-FastSurferCNN.utils.misc", false], [58, "module-FastSurferCNN.utils.parser_defaults", false], [59, "module-FastSurferCNN.utils.run_tools", false], [60, "module-FastSurferCNN.utils.threads", false], [61, "module-FastSurferCNN.version", false], [62, "module-HypVINN.data_loader.data_utils", false], [63, "module-HypVINN.data_loader.dataset", false], [64, "module-HypVINN.inference", false], [65, "module-HypVINN.models.networks", false], [66, "module-HypVINN.run_prediction", false], [67, "module-recon_surf.N4_bias_correct", false], [68, "module-recon_surf.align_points", false], [69, "module-recon_surf.align_seg", false], [70, "module-recon_surf.create_annotation", false], [71, "module-recon_surf.fs_balabels", false], [72, "module-recon_surf.lta", false], [73, "module-recon_surf.map_surf_label", false], [74, "module-recon_surf.paint_cc_into_pred", false], [75, "module-recon_surf.rewrite_mc_surface", false], [76, "module-recon_surf.rewrite_oriented_surface", false], [77, "module-recon_surf.rotate_sphere", false], [78, "module-recon_surf.sample_parc", false], [79, "module-recon_surf.smooth_aparc", false], [80, "module-recon_surf.spherically_project_wrapper", false]], "multiscaledataset (class in fastsurfercnn.data_loader.dataset)": [[35, "FastSurferCNN.data_loader.dataset.MultiScaleDataset", false]], "multiscaledatasetval (class in fastsurfercnn.data_loader.dataset)": [[35, "FastSurferCNN.data_loader.dataset.MultiScaleDatasetVal", false]], "multiscaleorigdatathickslices (class in fastsurfercnn.data_loader.dataset)": [[35, "FastSurferCNN.data_loader.dataset.MultiScaleOrigDataThickSlices", false]], "name (fastsurfercnn.utils.mapper.colorlookuptable property)": [[54, "FastSurferCNN.utils.mapper.ColorLookupTable.name", false]], "name (fastsurfercnn.utils.mapper.mapper property)": [[54, "FastSurferCNN.utils.mapper.Mapper.name", false]], "normalize_img() (in module recon_surf.n4_bias_correct)": [[67, "recon_surf.N4_bias_correct.normalize_img", false]], "normalize_wm_aseg() (in module recon_surf.n4_bias_correct)": [[67, "recon_surf.N4_bias_correct.normalize_wm_aseg", false]], "normalize_wm_mask_ball() (in module recon_surf.n4_bias_correct)": [[67, "recon_surf.N4_bias_correct.normalize_wm_mask_ball", false]], "option_parse() (in module hypvinn.run_prediction)": [[66, "HypVINN.run_prediction.option_parse", false]], "optional_path() (in module hypvinn.run_prediction)": [[66, "HypVINN.run_prediction.optional_path", false]], "options_parse() (in module fastsurfercnn.data_loader.conform)": [[33, "FastSurferCNN.data_loader.conform.options_parse", false]], "options_parse() (in module fastsurfercnn.quick_qc)": [[44, "FastSurferCNN.quick_qc.options_parse", false]], "options_parse() (in module fastsurfercnn.reduce_to_aseg)": [[45, "FastSurferCNN.reduce_to_aseg.options_parse", false]], "options_parse() (in module recon_surf.align_seg)": [[69, "recon_surf.align_seg.options_parse", false]], "options_parse() (in module recon_surf.create_annotation)": [[70, "recon_surf.create_annotation.options_parse", false]], "options_parse() (in module recon_surf.fs_balabels)": [[71, "recon_surf.fs_balabels.options_parse", false]], "options_parse() (in module recon_surf.map_surf_label)": [[73, "recon_surf.map_surf_label.options_parse", false]], "options_parse() (in module recon_surf.n4_bias_correct)": [[67, "recon_surf.N4_bias_correct.options_parse", false]], "options_parse() (in module recon_surf.rewrite_mc_surface)": [[75, "recon_surf.rewrite_mc_surface.options_parse", false]], "options_parse() (in module recon_surf.rotate_sphere)": [[77, "recon_surf.rotate_sphere.options_parse", false]], "options_parse() (in module recon_surf.sample_parc)": [[78, "recon_surf.sample_parc.options_parse", false]], "options_parse() (in module recon_surf.smooth_aparc)": [[79, "recon_surf.smooth_aparc.options_parse", false]], "orig_name (fastsurfercnn.utils.common.subjectdirectory property)": [[50, "FastSurferCNN.utils.common.SubjectDirectory.orig_name", false]], "outputdenseblock (class in fastsurfercnn.models.sub_module)": [[43, "FastSurferCNN.models.sub_module.OutputDenseBlock", false]], "pad_slicer() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.pad_slicer", false]], "paint_in_cc() (in module recon_surf.paint_cc_into_pred)": [[74, "recon_surf.paint_cc_into_pred.paint_in_cc", false]], "parse_build_file() (in module fastsurfercnn.version)": [[61, "FastSurferCNN.version.parse_build_file", false]], "parse_files() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.parse_files", false]], "parse_version() (in module recon_surf.fs_balabels)": [[71, "recon_surf.fs_balabels.parse_version", false]], "patch_filter() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.patch_filter", false]], "patch_neighbors() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.patch_neighbors", false]], "pipeline() (in module fastsurfercnn.utils.common)": [[50, "FastSurferCNN.utils.common.pipeline", false]], "pipeline_conform_and_save_orig() (fastsurfercnn.run_prediction.runmodelondata method)": [[46, "FastSurferCNN.run_prediction.RunModelOnData.pipeline_conform_and_save_orig", false]], "plane (cerebnet.data_loader.dataset.subjectdataset property)": [[16, "CerebNet.data_loader.dataset.SubjectDataset.plane", false]], "plot_confusion_matrix() (in module cerebnet.utils.misc)": [[31, "CerebNet.utils.misc.plot_confusion_matrix", false]], "plot_confusion_matrix() (in module fastsurfercnn.utils.misc)": [[57, "FastSurferCNN.utils.misc.plot_confusion_matrix", false]], "plot_predictions() (in module cerebnet.utils.misc)": [[31, "CerebNet.utils.misc.plot_predictions", false]], "plot_predictions() (in module fastsurfercnn.utils.misc)": [[57, "FastSurferCNN.utils.misc.plot_predictions", false]], "pool (fastsurfercnn.run_prediction.runmodelondata property)": [[46, "FastSurferCNN.run_prediction.RunModelOnData.pool", false]], "popen (class in fastsurfercnn.utils.run_tools)": [[59, "FastSurferCNN.utils.run_tools.Popen", false]], "precision_recall() (in module fastsurfercnn.utils.metrics)": [[56, "FastSurferCNN.utils.metrics.precision_recall", false]], "prediction_visualize() (cerebnet.utils.meters.meter method)": [[29, "CerebNet.utils.meters.Meter.prediction_visualize", false]], "prepare_checkpoints() (in module hypvinn.run_prediction)": [[66, "HypVINN.run_prediction.prepare_checkpoints", false]], "preproc_image() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.preproc_image", false]], "print_build_file() (in module fastsurfercnn.version)": [[61, "FastSurferCNN.version.print_build_file", false]], "pv_calc() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.pv_calc", false]], "pv_calc_patch() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.pv_calc_patch", false]], "pvstats (class in fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.PVStats", false]], "pypopen (class in fastsurfercnn.utils.run_tools)": [[59, "FastSurferCNN.utils.run_tools.PyPopen", false]], "randomaffine (class in cerebnet.data_loader.augmentation)": [[14, "CerebNet.data_loader.augmentation.RandomAffine", false]], "randombiasfield (class in cerebnet.data_loader.augmentation)": [[14, "CerebNet.data_loader.augmentation.RandomBiasField", false]], "randomflip (class in cerebnet.data_loader.augmentation)": [[14, "CerebNet.data_loader.augmentation.RandomFlip", false]], "randomlabelstoimage (class in cerebnet.data_loader.augmentation)": [[14, "CerebNet.data_loader.augmentation.RandomLabelsToImage", false]], "read_and_close_version() (in module fastsurfercnn.version)": [[61, "FastSurferCNN.version.read_and_close_version", false]], "read_classes_from_lut() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.read_classes_from_lut", false]], "read_colortable() (in module recon_surf.create_annotation)": [[70, "recon_surf.create_annotation.read_colortable", false]], "read_colortables() (in module recon_surf.fs_balabels)": [[71, "recon_surf.fs_balabels.read_colortables", false]], "read_lta() (in module cerebnet.datasets.utils)": [[20, "CerebNet.datasets.utils.read_lta", false]], "read_multiple_labels() (in module recon_surf.create_annotation)": [[70, "recon_surf.create_annotation.read_multiple_labels", false]], "read_talairach_xfm() (in module recon_surf.n4_bias_correct)": [[67, "recon_surf.N4_bias_correct.read_talairach_xfm", false]], "read_version_from_project_file() (in module fastsurfercnn.version)": [[61, "FastSurferCNN.version.read_version_from_project_file", false]], "recon_surf.align_points": [[68, "module-recon_surf.align_points", false]], "recon_surf.align_seg": [[69, "module-recon_surf.align_seg", false]], "recon_surf.create_annotation": [[70, "module-recon_surf.create_annotation", false]], "recon_surf.fs_balabels": [[71, "module-recon_surf.fs_balabels", false]], "recon_surf.lta": [[72, "module-recon_surf.lta", false]], "recon_surf.map_surf_label": [[73, "module-recon_surf.map_surf_label", false]], "recon_surf.n4_bias_correct": [[67, "module-recon_surf.N4_bias_correct", false]], "recon_surf.paint_cc_into_pred": [[74, "module-recon_surf.paint_cc_into_pred", false]], "recon_surf.rewrite_mc_surface": [[75, "module-recon_surf.rewrite_mc_surface", false]], "recon_surf.rewrite_oriented_surface": [[76, "module-recon_surf.rewrite_oriented_surface", false]], "recon_surf.rotate_sphere": [[77, "module-recon_surf.rotate_sphere", false]], "recon_surf.sample_parc": [[78, "module-recon_surf.sample_parc", false]], "recon_surf.smooth_aparc": [[79, "module-recon_surf.smooth_aparc", false]], "recon_surf.spherically_project_wrapper": [[80, "module-recon_surf.spherically_project_wrapper", false]], "reduce_to_aseg() (in module fastsurfercnn.reduce_to_aseg)": [[45, "FastSurferCNN.reduce_to_aseg.reduce_to_aseg", false]], "reducelronplateauwithrestarts (class in cerebnet.utils.lr_scheduler)": [[28, "CerebNet.utils.lr_scheduler.ReduceLROnPlateauWithRestarts", false]], "remove_ckpt() (in module fastsurfercnn.utils.checkpoint)": [[49, "FastSurferCNN.utils.checkpoint.remove_ckpt", false]], "reorient_img() (in module hypvinn.data_loader.data_utils)": [[62, "HypVINN.data_loader.data_utils.reorient_img", false]], "replace_labels() (in module recon_surf.sample_parc)": [[78, "recon_surf.sample_parc.replace_labels", false]], "resafe_surface() (in module recon_surf.rewrite_mc_surface)": [[75, "recon_surf.rewrite_mc_surface.resafe_surface", false]], "resafe_surface() (in module recon_surf.rewrite_oriented_surface)": [[76, "recon_surf.rewrite_oriented_surface.resafe_surface", false]], "rescale() (in module fastsurfercnn.data_loader.conform)": [[33, "FastSurferCNN.data_loader.conform.rescale", false]], "rescale_image() (in module hypvinn.data_loader.data_utils)": [[62, "HypVINN.data_loader.data_utils.rescale_image", false]], "reset() (cerebnet.utils.meters.meter method)": [[29, "CerebNet.utils.meters.Meter.reset", false]], "reset() (cerebnet.utils.metrics.dicescore method)": [[30, "CerebNet.utils.metrics.DiceScore.reset", false]], "reset() (fastsurfercnn.utils.meters.meter method)": [[55, "FastSurferCNN.utils.meters.Meter.reset", false]], "reset() (fastsurfercnn.utils.metrics.dicescore method)": [[56, "FastSurferCNN.utils.metrics.DiceScore.reset", false]], "reversed_dict() (fastsurfercnn.utils.mapper.mapper method)": [[54, "FastSurferCNN.utils.mapper.Mapper.reversed_dict", false]], "rmat2angles() (in module recon_surf.align_points)": [[68, "recon_surf.align_points.rmat2angles", false]], "roi (cerebnet.data_loader.dataset.subjectdataset attribute)": [[16, "CerebNet.data_loader.dataset.SubjectDataset.roi", false]], "run() (fastsurfercnn.inference.inference method)": [[39, "FastSurferCNN.inference.Inference.run", false]], "run() (hypvinn.inference.inference method)": [[64, "HypVINN.inference.Inference.run", false]], "runmodelondata (class in fastsurfercnn.run_prediction)": [[46, "FastSurferCNN.run_prediction.RunModelOnData", false]], "sagittal_coronal_remap_lookup() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.sagittal_coronal_remap_lookup", false]], "sample_img() (in module recon_surf.sample_parc)": [[78, "recon_surf.sample_parc.sample_img", false]], "sample_intensity_stats_from_image() (in module cerebnet.data_loader.augmentation)": [[14, "CerebNet.data_loader.augmentation.sample_intensity_stats_from_image", false]], "sample_nearest_nonzero() (in module recon_surf.sample_parc)": [[78, "recon_surf.sample_parc.sample_nearest_nonzero", false]], "sample_parc() (in module recon_surf.sample_parc)": [[78, "recon_surf.sample_parc.sample_parc", false]], "save_checkpoint() (in module cerebnet.utils.checkpoint)": [[26, "CerebNet.utils.checkpoint.save_checkpoint", false]], "save_checkpoint() (in module fastsurfercnn.utils.checkpoint)": [[49, "FastSurferCNN.utils.checkpoint.save_checkpoint", false]], "save_image() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.save_image", false]], "save_img() (fastsurfercnn.run_prediction.runmodelondata method)": [[46, "FastSurferCNN.run_prediction.RunModelOnData.save_img", false]], "save_mgh_image() (in module cerebnet.datasets.wm_merge_clean)": [[21, "CerebNet.datasets.wm_merge_clean.save_mgh_image", false]], "save_nii_image() (in module cerebnet.apply_warp)": [[13, "CerebNet.apply_warp.save_nii_image", false]], "scalecrop() (in module fastsurfercnn.data_loader.conform)": [[33, "FastSurferCNN.data_loader.conform.scalecrop", false]], "section() (in module fastsurfercnn.version)": [[61, "FastSurferCNN.version.section", false]], "seg_borders() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.seg_borders", false]], "segfile (fastsurfercnn.utils.common.subjectdirectory property)": [[50, "FastSurferCNN.utils.common.SubjectDirectory.segfile", false]], "serialexecutor (class in fastsurfercnn.utils.common)": [[50, "FastSurferCNN.utils.common.SerialExecutor", false]], "set_cfg() (fastsurfercnn.inference.inference method)": [[39, "FastSurferCNN.inference.Inference.set_cfg", false]], "set_cfg() (hypvinn.inference.inference method)": [[64, "HypVINN.inference.Inference.set_cfg", false]], "set_lr() (cerebnet.utils.lr_scheduler.cosinelr method)": [[28, "CerebNet.utils.lr_scheduler.CosineLR.set_lr", false]], "set_model() (fastsurfercnn.run_prediction.runmodelondata method)": [[46, "FastSurferCNN.run_prediction.RunModelOnData.set_model", false]], "set_model() (hypvinn.inference.inference method)": [[64, "HypVINN.inference.Inference.set_model", false]], "set_plane() (cerebnet.data_loader.dataset.subjectdataset method)": [[16, "CerebNet.data_loader.dataset.SubjectDataset.set_plane", false]], "set_summary_path() (in module cerebnet.utils.misc)": [[31, "CerebNet.utils.misc.set_summary_path", false]], "set_up_cfgs() (in module fastsurfercnn.run_prediction)": [[46, "FastSurferCNN.run_prediction.set_up_cfgs", false]], "set_up_cfgs() (in module hypvinn.run_prediction)": [[66, "HypVINN.run_prediction.set_up_cfgs", false]], "set_up_model_params() (fastsurfercnn.run_prediction.runmodelondata method)": [[46, "FastSurferCNN.run_prediction.RunModelOnData.set_up_model_params", false]], "setup_logging() (in module fastsurfercnn.utils.logging)": [[52, "FastSurferCNN.utils.logging.setup_logging", false]], "setup_model() (fastsurfercnn.inference.inference method)": [[39, "FastSurferCNN.inference.Inference.setup_model", false]], "setup_model() (hypvinn.inference.inference method)": [[64, "HypVINN.inference.Inference.setup_model", false]], "setup_options() (in module cerebnet.run_prediction)": [[25, "CerebNet.run_prediction.setup_options", false]], "setup_options() (in module recon_surf.spherically_project_wrapper)": [[80, "recon_surf.spherically_project_wrapper.setup_options", false]], "slice_lia2ras() (in module cerebnet.data_loader.data_utils)": [[15, "CerebNet.data_loader.data_utils.slice_lia2ras", false]], "slice_ras2lia() (in module cerebnet.data_loader.data_utils)": [[15, "CerebNet.data_loader.data_utils.slice_ras2lia", false]], "smooth_aparc() (in module recon_surf.smooth_aparc)": [[79, "recon_surf.smooth_aparc.smooth_aparc", false]], "source_space (fastsurfercnn.utils.mapper.mapper property)": [[54, "FastSurferCNN.utils.mapper.Mapper.source_space", false]], "sphere() (in module cerebnet.datasets.wm_merge_clean)": [[21, "CerebNet.datasets.wm_merge_clean.sphere", false]], "spherical_wrapper() (in module recon_surf.spherically_project_wrapper)": [[80, "recon_surf.spherically_project_wrapper.spherical_wrapper", false]], "split_cortex_labels() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.split_cortex_labels", false]], "step() (cerebnet.utils.lr_scheduler.reducelronplateauwithrestarts method)": [[28, "CerebNet.utils.lr_scheduler.ReduceLROnPlateauWithRestarts.step", false]], "subject_dir (fastsurfercnn.utils.common.subjectdirectory property)": [[50, "FastSurferCNN.utils.common.SubjectDirectory.subject_dir", false]], "subjectdataset (class in cerebnet.data_loader.dataset)": [[16, "CerebNet.data_loader.dataset.SubjectDataset", false]], "subjectdirectory (class in fastsurfercnn.utils.common)": [[50, "FastSurferCNN.utils.common.SubjectDirectory", false]], "subjectdirectoryconfig (class in fastsurfercnn.utils.parser_defaults)": [[58, "FastSurferCNN.utils.parser_defaults.SubjectDirectoryConfig", false]], "subjectlist (class in fastsurfercnn.utils.common)": [[50, "FastSurferCNN.utils.common.SubjectList", false]], "subjectloader (class in cerebnet.datasets.load_data)": [[19, "CerebNet.datasets.load_data.SubjectLoader", false]], "submit() (fastsurfercnn.utils.common.serialexecutor method)": [[50, "FastSurferCNN.utils.common.SerialExecutor.submit", false]], "table_to_dataframe() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.table_to_dataframe", false]], "target_dtype() (in module fastsurfercnn.utils.arg_types)": [[48, "FastSurferCNN.utils.arg_types.target_dtype", false]], "target_space (fastsurfercnn.utils.mapper.mapper property)": [[54, "FastSurferCNN.utils.mapper.Mapper.target_space", false]], "testloader (class in cerebnet.data_loader.dataset)": [[16, "CerebNet.data_loader.dataset.TestLoader", false]], "testmeter (class in cerebnet.utils.meters)": [[29, "CerebNet.utils.meters.TestMeter", false]], "to() (fastsurfercnn.inference.inference method)": [[39, "FastSurferCNN.inference.Inference.to", false]], "to_same_type() (in module fastsurfercnn.utils.mapper)": [[54, "FastSurferCNN.utils.mapper.to_same_type", false]], "totensor (class in cerebnet.data_loader.augmentation)": [[14, "CerebNet.data_loader.augmentation.ToTensor", false]], "totensor (class in fastsurfercnn.data_loader.augmentation)": [[32, "FastSurferCNN.data_loader.augmentation.ToTensor", false]], "totensortest (class in cerebnet.data_loader.augmentation)": [[14, "CerebNet.data_loader.augmentation.ToTensorTest", false]], "totensortest (class in fastsurfercnn.data_loader.augmentation)": [[32, "FastSurferCNN.data_loader.augmentation.ToTensorTest", false]], "transform() (fastsurfercnn.generate_hdf5.h5pydataset method)": [[38, "FastSurferCNN.generate_hdf5.H5pyDataset.transform", false]], "transform_axial() (in module cerebnet.data_loader.data_utils)": [[15, "CerebNet.data_loader.data_utils.transform_axial", false]], "transform_axial() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.transform_axial", false]], "transform_axial2coronal() (in module hypvinn.data_loader.data_utils)": [[62, "HypVINN.data_loader.data_utils.transform_axial2coronal", false]], "transform_axial2sagittal() (in module cerebnet.data_loader.data_utils)": [[15, "CerebNet.data_loader.data_utils.transform_axial2sagittal", false]], "transform_axial2sagittal() (in module hypvinn.data_loader.data_utils)": [[62, "HypVINN.data_loader.data_utils.transform_axial2sagittal", false]], "transform_coronal() (in module cerebnet.data_loader.data_utils)": [[15, "CerebNet.data_loader.data_utils.transform_coronal", false]], "transform_sagittal() (in module cerebnet.data_loader.data_utils)": [[15, "CerebNet.data_loader.data_utils.transform_sagittal", false]], "transform_sagittal() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.transform_sagittal", false]], "tsvlookuptable (class in fastsurfercnn.utils.mapper)": [[54, "FastSurferCNN.utils.mapper.TSVLookupTable", false]], "uniform_filter() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.uniform_filter", false]], "unify_imgs() (fastsurfercnn.data_loader.dataset.multiscaledataset method)": [[35, "FastSurferCNN.data_loader.dataset.MultiScaleDataset.unify_imgs", false]], "unify_lateralized_labels() (in module fastsurfercnn.data_loader.data_utils)": [[34, "FastSurferCNN.data_loader.data_utils.unify_lateralized_labels", false]], "unquote_str() (in module fastsurfercnn.utils.arg_types)": [[48, "FastSurferCNN.utils.arg_types.unquote_str", false]], "update() (cerebnet.utils.metrics.dicescore method)": [[30, "CerebNet.utils.metrics.DiceScore.update", false]], "update() (fastsurfercnn.utils.mapper.mapper method)": [[54, "FastSurferCNN.utils.mapper.Mapper.update", false]], "update() (fastsurfercnn.utils.metrics.dicescore method)": [[56, "FastSurferCNN.utils.metrics.DiceScore.update", false]], "update_num_steps() (in module fastsurfercnn.utils.misc)": [[57, "FastSurferCNN.utils.misc.update_num_steps", false]], "update_results_dir() (in module cerebnet.utils.misc)": [[31, "CerebNet.utils.misc.update_results_dir", false]], "update_split_path() (in module cerebnet.utils.misc)": [[31, "CerebNet.utils.misc.update_split_path", false]], "update_stats() (cerebnet.utils.meters.meter method)": [[29, "CerebNet.utils.meters.Meter.update_stats", false]], "update_stats() (fastsurfercnn.utils.meters.meter method)": [[55, "FastSurferCNN.utils.meters.Meter.update_stats", false]], "update_structnames() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.update_structnames", false]], "versiondict (class in fastsurfercnn.version)": [[61, "FastSurferCNN.version.VersionDict", false]], "visualize_batch() (in module cerebnet.utils.misc)": [[31, "CerebNet.utils.misc.visualize_batch", false]], "volume_similarity() (in module cerebnet.utils.metrics)": [[30, "CerebNet.utils.metrics.volume_similarity", false]], "vox_size() (in module fastsurfercnn.utils.arg_types)": [[48, "FastSurferCNN.utils.arg_types.vox_size", false]], "warmupcosinelr (class in cerebnet.utils.lr_scheduler)": [[28, "CerebNet.utils.lr_scheduler.WarmupCosineLR", false]], "write_annot() (in module recon_surf.create_annotation)": [[70, "recon_surf.create_annotation.write_annot", false]], "write_statsfile() (in module fastsurfercnn.segstats)": [[47, "FastSurferCNN.segstats.write_statsfile", false]], "write_summary() (cerebnet.utils.meters.meter method)": [[29, "CerebNet.utils.meters.Meter.write_summary", false]], "write_summary() (fastsurfercnn.utils.meters.meter method)": [[55, "FastSurferCNN.utils.meters.Meter.write_summary", false]], "writelta() (in module recon_surf.lta)": [[72, "recon_surf.lta.writeLTA", false]], "writesurflabel() (in module recon_surf.map_surf_label)": [[73, "recon_surf.map_surf_label.writeSurfLabel", false]], "zeropad2d (class in fastsurfercnn.data_loader.augmentation)": [[32, "FastSurferCNN.data_loader.augmentation.ZeroPad2D", false]], "zeropad2dtest (class in fastsurfercnn.data_loader.augmentation)": [[32, "FastSurferCNN.data_loader.augmentation.ZeroPad2DTest", false]], "zoom2d (class in fastsurfercnn.models.interpolation_layer)": [[40, "FastSurferCNN.models.interpolation_layer.Zoom2d", false]], "zoom3d (class in fastsurfercnn.models.interpolation_layer)": [[40, "FastSurferCNN.models.interpolation_layer.Zoom3d", false]]}, "objects": {"CerebNet": [[13, 0, 0, "-", "apply_warp"], [22, 0, 0, "-", "inference"], [25, 0, 0, "-", "run_prediction"]], "CerebNet.apply_warp": [[13, 1, 1, "", "main"], [13, 1, 1, "", "save_nii_image"]], "CerebNet.data_loader": [[14, 0, 0, "-", "augmentation"], [15, 0, 0, "-", "data_utils"], [16, 0, 0, "-", "dataset"], [17, 0, 0, "-", "loader"]], "CerebNet.data_loader.augmentation": [[14, 2, 1, "", "RandomAffine"], [14, 2, 1, "", "RandomBiasField"], [14, 2, 1, "", "RandomFlip"], [14, 2, 1, "", "RandomLabelsToImage"], [14, 2, 1, "", "ToTensor"], [14, 2, 1, "", "ToTensorTest"], [14, 1, 1, "", "sample_intensity_stats_from_image"]], "CerebNet.data_loader.data_utils": [[15, 1, 1, "", "create_weight_mask2d"], [15, 1, 1, "", "filter_blank_slices_thick"], [15, 1, 1, "", "get_aseg_cereb_mask"], [15, 1, 1, "", "map_prediction_sagittal2full"], [15, 1, 1, "", "map_sag2label"], [15, 1, 1, "", "slice_lia2ras"], [15, 1, 1, "", "slice_ras2lia"], [15, 1, 1, "", "transform_axial"], [15, 1, 1, "", "transform_axial2sagittal"], [15, 1, 1, "", "transform_coronal"], [15, 1, 1, "", "transform_sagittal"]], "CerebNet.data_loader.dataset": [[16, 2, 1, "", "CerebDataset"], [16, 2, 1, "", "SubjectDataset"], [16, 2, 1, "", "TestLoader"]], "CerebNet.data_loader.dataset.SubjectDataset": [[16, 3, 1, "", "locate_mask_bbox"], [16, 4, 1, "", "plane"], [16, 5, 1, "", "roi"], [16, 3, 1, "", "set_plane"]], "CerebNet.data_loader.loader": [[17, 1, 1, "", "get_dataloader"]], "CerebNet.datasets": [[18, 0, 0, "-", "generate_hdf5"], [19, 0, 0, "-", "load_data"], [20, 0, 0, "-", "utils"], [21, 0, 0, "-", "wm_merge_clean"]], "CerebNet.datasets.generate_hdf5": [[18, 2, 1, "", "CerebNetDataset"]], "CerebNet.datasets.generate_hdf5.CerebNetDataset": [[18, 3, 1, "", "create_hdf5_dataset"]], "CerebNet.datasets.load_data": [[19, 2, 1, "", "SubjectLoader"]], "CerebNet.datasets.load_data.SubjectLoader": [[19, 3, 1, "", "load_subject"], [19, 3, 1, "", "load_test_subject"]], "CerebNet.datasets.utils": [[20, 2, 1, "", "LTADict"], [20, 1, 1, "", "bounding_volume_offset"], [20, 1, 1, "", "crop_transform"], [20, 1, 1, "", "filter_blank_slices_thick"], [20, 1, 1, "", "map_label2subseg"], [20, 1, 1, "", "map_size"], [20, 1, 1, "", "read_lta"]], "CerebNet.datasets.wm_merge_clean": [[21, 1, 1, "", "add_cereb_wm"], [21, 1, 1, "", "cereb_subseg_lateral_mask"], [21, 1, 1, "", "correct_cereb_brainstem"], [21, 1, 1, "", "drop_disconnected_component"], [21, 1, 1, "", "filling_unknown_labels"], [21, 1, 1, "", "locating_unknowns"], [21, 1, 1, "", "save_mgh_image"], [21, 1, 1, "", "sphere"]], "CerebNet.inference": [[22, 2, 1, "", "Inference"]], "CerebNet.models": [[23, 0, 0, "-", "networks"], [24, 0, 0, "-", "sub_module"]], "CerebNet.models.networks": [[23, 2, 1, "", "FastSurferCNN"], [23, 1, 1, "", "build_model"]], "CerebNet.models.networks.FastSurferCNN": [[23, 3, 1, "", "forward"]], "CerebNet.models.sub_module": [[24, 2, 1, "", "ClassifierBlock"], [24, 2, 1, "", "CompetitiveDecoderBlock"], [24, 2, 1, "", "CompetitiveDenseBlock"], [24, 2, 1, "", "CompetitiveDenseBlockInput"], [24, 2, 1, "", "CompetitiveEncoderBlock"], [24, 2, 1, "", "CompetitiveEncoderBlockInput"]], "CerebNet.models.sub_module.ClassifierBlock": [[24, 3, 1, "", "forward"]], "CerebNet.models.sub_module.CompetitiveDecoderBlock": [[24, 3, 1, "", "forward"]], "CerebNet.models.sub_module.CompetitiveDenseBlock": [[24, 3, 1, "", "forward"]], "CerebNet.models.sub_module.CompetitiveDenseBlockInput": [[24, 3, 1, "", "forward"]], "CerebNet.models.sub_module.CompetitiveEncoderBlock": [[24, 3, 1, "", "forward"]], "CerebNet.models.sub_module.CompetitiveEncoderBlockInput": [[24, 3, 1, "", "forward"]], "CerebNet.run_prediction": [[25, 1, 1, "", "main"], [25, 1, 1, "", "setup_options"]], "CerebNet.utils": [[26, 0, 0, "-", "checkpoint"], [27, 0, 0, "-", "load_config"], [28, 0, 0, "-", "lr_scheduler"], [29, 0, 0, "-", "meters"], [30, 0, 0, "-", "metrics"], [31, 0, 0, "-", "misc"]], "CerebNet.utils.checkpoint": [[26, 1, 1, "", "create_checkpoint_dir"], [26, 1, 1, "", "get_checkpoint"], [26, 1, 1, "", "get_checkpoint_path"], [26, 1, 1, "", "is_checkpoint_epoch"], [26, 1, 1, "", "load_from_checkpoint"], [26, 1, 1, "", "save_checkpoint"]], "CerebNet.utils.load_config": [[27, 1, 1, "", "get_config"]], "CerebNet.utils.lr_scheduler": [[28, 2, 1, "", "CosineAnnealingWarmRestartsDecay"], [28, 2, 1, "", "CosineLR"], [28, 2, 1, "", "ReduceLROnPlateauWithRestarts"], [28, 2, 1, "", "WarmupCosineLR"], [28, 1, 1, "", "get_lr_scheduler"]], "CerebNet.utils.lr_scheduler.CosineAnnealingWarmRestartsDecay": [[28, 3, 1, "", "decay_base_lr"]], "CerebNet.utils.lr_scheduler.CosineLR": [[28, 3, 1, "", "get_epoch_lr"], [28, 3, 1, "", "lr_func_cosine"], [28, 3, 1, "", "set_lr"]], "CerebNet.utils.lr_scheduler.ReduceLROnPlateauWithRestarts": [[28, 3, 1, "", "step"]], "CerebNet.utils.lr_scheduler.WarmupCosineLR": [[28, 3, 1, "", "get_lr"]], "CerebNet.utils.meters": [[29, 2, 1, "", "Meter"], [29, 2, 1, "", "TestMeter"]], "CerebNet.utils.meters.Meter": [[29, 3, 1, "", "log_epoch"], [29, 3, 1, "", "log_iter"], [29, 3, 1, "", "log_lr"], [29, 3, 1, "", "prediction_visualize"], [29, 3, 1, "", "reset"], [29, 3, 1, "", "update_stats"], [29, 3, 1, "", "write_summary"]], "CerebNet.utils.meters.TestMeter": [[29, 3, 1, "", "metrics_per_class"]], "CerebNet.utils.metrics": [[30, 2, 1, "", "DiceScore"], [30, 1, 1, "", "dice_score"], [30, 1, 1, "", "hd"], [30, 1, 1, "", "hd95"], [30, 1, 1, "", "volume_similarity"]], "CerebNet.utils.metrics.DiceScore": [[30, 3, 1, "", "compute"], [30, 3, 1, "", "reset"], [30, 3, 1, "", "update"]], "CerebNet.utils.misc": [[31, 1, 1, "", "load_classwise_weights"], [31, 1, 1, "", "plot_confusion_matrix"], [31, 1, 1, "", "plot_predictions"], [31, 1, 1, "", "set_summary_path"], [31, 1, 1, "", "update_results_dir"], [31, 1, 1, "", "update_split_path"], [31, 1, 1, "", "visualize_batch"]], "FastSurferCNN": [[37, 0, 0, "-", "download_checkpoints"], [38, 0, 0, "-", "generate_hdf5"], [39, 0, 0, "-", "inference"], [44, 0, 0, "-", "quick_qc"], [45, 0, 0, "-", "reduce_to_aseg"], [46, 0, 0, "-", "run_prediction"], [47, 0, 0, "-", "segstats"], [61, 0, 0, "-", "version"]], "FastSurferCNN.data_loader": [[32, 0, 0, "-", "augmentation"], [33, 0, 0, "-", "conform"], [34, 0, 0, "-", "data_utils"], [35, 0, 0, "-", "dataset"], [36, 0, 0, "-", "loader"]], "FastSurferCNN.data_loader.augmentation": [[32, 2, 1, "", "AddGaussianNoise"], [32, 2, 1, "", "AugmentationPadImage"], [32, 2, 1, "", "AugmentationRandomCrop"], [32, 2, 1, "", "ToTensor"], [32, 2, 1, "", "ToTensorTest"], [32, 2, 1, "", "ZeroPad2D"], [32, 2, 1, "", "ZeroPad2DTest"]], "FastSurferCNN.data_loader.conform": [[33, 2, 1, "", "Criteria"], [33, 1, 1, "", "check_affine_in_nifti"], [33, 1, 1, "", "conform"], [33, 1, 1, "", "find_img_size_by_fov"], [33, 1, 1, "", "find_min_size"], [33, 1, 1, "", "get_conformed_vox_img_size"], [33, 1, 1, "", "getscale"], [33, 1, 1, "", "is_conform"], [33, 1, 1, "", "is_lia"], [33, 1, 1, "", "is_resampling_vox2vox"], [33, 1, 1, "", "make_parser"], [33, 1, 1, "", "map_image"], [33, 1, 1, "", "options_parse"], [33, 1, 1, "", "rescale"], [33, 1, 1, "", "scalecrop"]], "FastSurferCNN.data_loader.data_utils": [[34, 1, 1, "", "bbox_3d"], [34, 1, 1, "", "clean_cortex_labels"], [34, 1, 1, "", "cortex_border_mask"], [34, 1, 1, "", "create_weight_mask"], [34, 1, 1, "", "deep_sulci_and_wm_strand_mask"], [34, 1, 1, "", "fill_unknown_labels_per_hemi"], [34, 1, 1, "", "filter_blank_slices_thick"], [34, 1, 1, "", "fuse_cortex_labels"], [34, 1, 1, "", "get_labels_from_lut"], [34, 1, 1, "", "get_largest_cc"], [34, 1, 1, "", "get_thick_slices"], [34, 1, 1, "", "infer_mapping_from_lut"], [34, 1, 1, "", "load_and_conform_image"], [34, 1, 1, "", "load_image"], [34, 1, 1, "", "load_maybe_conform"], [34, 1, 1, "", "map_aparc_aseg2label"], [34, 1, 1, "", "map_label2aparc_aseg"], [34, 1, 1, "", "map_prediction_sagittal2full"], [34, 1, 1, "", "read_classes_from_lut"], [34, 1, 1, "", "sagittal_coronal_remap_lookup"], [34, 1, 1, "", "save_image"], [34, 1, 1, "", "split_cortex_labels"], [34, 1, 1, "", "transform_axial"], [34, 1, 1, "", "transform_sagittal"], [34, 1, 1, "", "unify_lateralized_labels"]], "FastSurferCNN.data_loader.dataset": [[35, 2, 1, "", "MultiScaleDataset"], [35, 2, 1, "", "MultiScaleDatasetVal"], [35, 2, 1, "", "MultiScaleOrigDataThickSlices"]], "FastSurferCNN.data_loader.dataset.MultiScaleDataset": [[35, 3, 1, "", "get_subject_names"], [35, 3, 1, "", "unify_imgs"]], "FastSurferCNN.data_loader.dataset.MultiScaleDatasetVal": [[35, 3, 1, "", "get_subject_names"]], "FastSurferCNN.data_loader.loader": [[36, 1, 1, "", "get_dataloader"]], "FastSurferCNN.generate_hdf5": [[38, 2, 1, "", "H5pyDataset"]], "FastSurferCNN.generate_hdf5.H5pyDataset": [[38, 3, 1, "", "create_hdf5_dataset"], [38, 3, 1, "", "transform"]], "FastSurferCNN.inference": [[39, 2, 1, "", "Inference"]], "FastSurferCNN.inference.Inference": [[39, 3, 1, "", "eval"], [39, 3, 1, "", "get_cfg"], [39, 3, 1, "", "get_device"], [39, 3, 1, "", "get_max_size"], [39, 3, 1, "", "get_model_height"], [39, 3, 1, "", "get_model_width"], [39, 3, 1, "", "get_modelname"], [39, 3, 1, "", "get_num_classes"], [39, 3, 1, "", "get_plane"], [39, 3, 1, "", "load_checkpoint"], [39, 3, 1, "", "run"], [39, 3, 1, "", "set_cfg"], [39, 3, 1, "", "setup_model"], [39, 3, 1, "", "to"]], "FastSurferCNN.models": [[40, 0, 0, "-", "interpolation_layer"], [41, 0, 0, "-", "losses"], [42, 0, 0, "-", "networks"], [43, 0, 0, "-", "sub_module"]], "FastSurferCNN.models.interpolation_layer": [[40, 2, 1, "", "Zoom2d"], [40, 2, 1, "", "Zoom3d"]], "FastSurferCNN.models.interpolation_layer.Zoom2d": [[40, 4, 1, "", "crop_position"]], "FastSurferCNN.models.interpolation_layer.Zoom3d": [[40, 4, 1, "", "crop_position"]], "FastSurferCNN.models.losses": [[41, 2, 1, "", "CombinedLoss"], [41, 2, 1, "", "CrossEntropy2D"], [41, 2, 1, "", "DiceLoss"], [41, 1, 1, "", "get_loss_func"]], "FastSurferCNN.models.losses.CombinedLoss": [[41, 3, 1, "", "forward"]], "FastSurferCNN.models.losses.CrossEntropy2D": [[41, 3, 1, "", "forward"]], "FastSurferCNN.models.losses.DiceLoss": [[41, 3, 1, "", "forward"]], "FastSurferCNN.models.networks": [[42, 2, 1, "", "FastSurferCNN"], [42, 2, 1, "", "FastSurferCNNBase"], [42, 2, 1, "", "FastSurferVINN"], [42, 1, 1, "", "build_model"]], "FastSurferCNN.models.networks.FastSurferCNN": [[42, 3, 1, "", "forward"]], "FastSurferCNN.models.networks.FastSurferCNNBase": [[42, 3, 1, "", "forward"]], "FastSurferCNN.models.networks.FastSurferVINN": [[42, 3, 1, "", "forward"]], "FastSurferCNN.models.sub_module": [[43, 2, 1, "", "ClassifierBlock"], [43, 2, 1, "", "CompetitiveDecoderBlock"], [43, 2, 1, "", "CompetitiveDenseBlock"], [43, 2, 1, "", "CompetitiveDenseBlockInput"], [43, 2, 1, "", "CompetitiveEncoderBlock"], [43, 2, 1, "", "CompetitiveEncoderBlockInput"], [43, 2, 1, "", "GaussianNoise"], [43, 2, 1, "", "InputDenseBlock"], [43, 2, 1, "", "OutputDenseBlock"]], "FastSurferCNN.models.sub_module.ClassifierBlock": [[43, 3, 1, "", "forward"]], "FastSurferCNN.models.sub_module.CompetitiveDecoderBlock": [[43, 3, 1, "", "forward"]], "FastSurferCNN.models.sub_module.CompetitiveDenseBlock": [[43, 3, 1, "", "forward"]], "FastSurferCNN.models.sub_module.CompetitiveDenseBlockInput": [[43, 3, 1, "", "forward"]], "FastSurferCNN.models.sub_module.CompetitiveEncoderBlock": [[43, 3, 1, "", "forward"]], "FastSurferCNN.models.sub_module.CompetitiveEncoderBlockInput": [[43, 3, 1, "", "forward"]], "FastSurferCNN.models.sub_module.GaussianNoise": [[43, 3, 1, "", "forward"]], "FastSurferCNN.models.sub_module.InputDenseBlock": [[43, 3, 1, "", "forward"]], "FastSurferCNN.models.sub_module.OutputDenseBlock": [[43, 3, 1, "", "forward"]], "FastSurferCNN.quick_qc": [[44, 1, 1, "", "check_volume"], [44, 1, 1, "", "get_region_bg_intersection_mask"], [44, 1, 1, "", "get_ventricle_bg_intersection_volume"], [44, 1, 1, "", "options_parse"]], "FastSurferCNN.reduce_to_aseg": [[45, 1, 1, "", "create_mask"], [45, 1, 1, "", "flip_wm_islands"], [45, 1, 1, "", "options_parse"], [45, 1, 1, "", "reduce_to_aseg"]], "FastSurferCNN.run_prediction": [[46, 2, 1, "", "RunModelOnData"], [46, 1, 1, "", "args2cfg"], [46, 1, 1, "", "make_parser"], [46, 1, 1, "", "set_up_cfgs"]], "FastSurferCNN.run_prediction.RunModelOnData": [[46, 3, 1, "", "async_save_img"], [46, 3, 1, "", "conform_and_save_orig"], [46, 3, 1, "", "get_num_classes"], [46, 3, 1, "", "get_prediction"], [46, 3, 1, "", "pipeline_conform_and_save_orig"], [46, 4, 1, "", "pool"], [46, 3, 1, "", "save_img"], [46, 3, 1, "", "set_model"], [46, 3, 1, "", "set_up_model_params"]], "FastSurferCNN.segstats": [[47, 2, 1, "", "HelpFormatter"], [47, 2, 1, "", "PVStats"], [47, 1, 1, "", "add_measure_parser"], [47, 1, 1, "", "add_two_help_messages"], [47, 1, 1, "", "borders"], [47, 1, 1, "", "calculate_merged_labels"], [47, 1, 1, "", "check_shape_affine"], [47, 1, 1, "", "crop_patch_to_mask"], [47, 1, 1, "", "empty"], [47, 1, 1, "", "format_parameters"], [47, 1, 1, "", "global_stats"], [47, 1, 1, "", "infer_labels_excludeid"], [47, 1, 1, "", "infer_merged_labels"], [47, 1, 1, "", "main"], [47, 1, 1, "", "make_arguments"], [47, 1, 1, "", "pad_slicer"], [47, 1, 1, "", "parse_files"], [47, 1, 1, "", "patch_filter"], [47, 1, 1, "", "patch_neighbors"], [47, 1, 1, "", "preproc_image"], [47, 1, 1, "", "pv_calc"], [47, 1, 1, "", "pv_calc_patch"], [47, 1, 1, "", "seg_borders"], [47, 1, 1, "", "table_to_dataframe"], [47, 1, 1, "", "uniform_filter"], [47, 1, 1, "", "update_structnames"], [47, 1, 1, "", "write_statsfile"]], "FastSurferCNN.utils": [[48, 0, 0, "-", "arg_types"], [49, 0, 0, "-", "checkpoint"], [50, 0, 0, "-", "common"], [51, 0, 0, "-", "load_config"], [52, 0, 0, "-", "logging"], [53, 0, 0, "-", "lr_scheduler"], [54, 0, 0, "-", "mapper"], [55, 0, 0, "-", "meters"], [56, 0, 0, "-", "metrics"], [57, 0, 0, "-", "misc"], [58, 0, 0, "-", "parser_defaults"], [59, 0, 0, "-", "run_tools"], [60, 0, 0, "-", "threads"]], "FastSurferCNN.utils.arg_types": [[48, 1, 1, "", "float_gt_zero_and_le_one"], [48, 1, 1, "", "int_ge_zero"], [48, 1, 1, "", "int_gt_zero"], [48, 1, 1, "", "target_dtype"], [48, 1, 1, "", "unquote_str"], [48, 1, 1, "", "vox_size"]], "FastSurferCNN.utils.checkpoint": [[49, 2, 1, "", "CheckpointConfigDict"], [49, 1, 1, "", "check_and_download_ckpts"], [49, 1, 1, "", "create_checkpoint_dir"], [49, 1, 1, "", "download_checkpoint"], [49, 1, 1, "", "get_checkpoint"], [49, 1, 1, "", "get_checkpoint_path"], [49, 1, 1, "", "get_checkpoints"], [49, 1, 1, "", "load_checkpoint_config"], [49, 1, 1, "", "load_checkpoint_config_defaults"], [49, 1, 1, "", "load_from_checkpoint"], [49, 1, 1, "", "remove_ckpt"], [49, 1, 1, "", "save_checkpoint"]], "FastSurferCNN.utils.common": [[50, 2, 1, "", "SerialExecutor"], [50, 2, 1, "", "SubjectDirectory"], [50, 2, 1, "", "SubjectList"], [50, 1, 1, "", "assert_no_root"], [50, 1, 1, "", "find_device"], [50, 1, 1, "", "handle_cuda_memory_exception"], [50, 1, 1, "", "iterate"], [50, 1, 1, "", "pipeline"]], "FastSurferCNN.utils.common.SerialExecutor": [[50, 3, 1, "", "map"], [50, 3, 1, "", "submit"]], "FastSurferCNN.utils.common.SubjectDirectory": [[50, 4, 1, "", "asegdkt_segfile"], [50, 3, 1, "", "can_resolve_attribute"], [50, 3, 1, "", "can_resolve_filename"], [50, 4, 1, "", "conf_name"], [50, 4, 1, "", "copy_orig_name"], [50, 3, 1, "", "fileexists_by_attribute"], [50, 3, 1, "", "fileexists_in_subject_folder"], [50, 3, 1, "", "filename_by_attribute"], [50, 3, 1, "", "filename_in_subject_folder"], [50, 3, 1, "", "get_attribute"], [50, 3, 1, "", "has_attribute"], [50, 4, 1, "", "id"], [50, 4, 1, "", "main_segfile"], [50, 4, 1, "", "orig_name"], [50, 4, 1, "", "segfile"], [50, 4, 1, "", "subject_dir"]], "FastSurferCNN.utils.common.SubjectList": [[50, 3, 1, "", "are_all_subject_files"], [50, 4, 1, "", "flags"], [50, 3, 1, "", "get_common_suffix"], [50, 3, 1, "", "make_subjects_dir"]], "FastSurferCNN.utils.load_config": [[51, 1, 1, "", "get_config"], [51, 1, 1, "", "load_config"]], "FastSurferCNN.utils.logging": [[52, 1, 1, "", "setup_logging"]], "FastSurferCNN.utils.lr_scheduler": [[53, 1, 1, "", "get_lr_scheduler"]], "FastSurferCNN.utils.mapper": [[54, 2, 1, "", "ColorLookupTable"], [54, 2, 1, "", "JsonColorLookupTable"], [54, 2, 1, "", "Mapper"], [54, 2, 1, "", "TSVLookupTable"], [54, 1, 1, "", "is_int"], [54, 1, 1, "", "to_same_type"]], "FastSurferCNN.utils.mapper.ColorLookupTable": [[54, 4, 1, "", "classes"], [54, 4, 1, "", "color_palette"], [54, 3, 1, "", "colormap"], [54, 3, 1, "", "get_color_by_index"], [54, 3, 1, "", "getitem_by_index"], [54, 3, 1, "", "labelname2id"], [54, 3, 1, "", "labelname2index"], [54, 4, 1, "", "name"]], "FastSurferCNN.utils.mapper.JsonColorLookupTable": [[54, 3, 1, "", "dataframe"], [54, 3, 1, "", "labelname2id"]], "FastSurferCNN.utils.mapper.Mapper": [[54, 3, 1, "", "chain"], [54, 3, 1, "", "is_bijective"], [54, 3, 1, "", "make_classmapper"], [54, 3, 1, "", "map"], [54, 4, 1, "", "max_label"], [54, 4, 1, "", "name"], [54, 3, 1, "", "reversed_dict"], [54, 4, 1, "", "source_space"], [54, 4, 1, "", "target_space"], [54, 3, 1, "", "update"]], "FastSurferCNN.utils.mapper.TSVLookupTable": [[54, 3, 1, "", "dataframe"], [54, 3, 1, "", "getitem_by_index"], [54, 3, 1, "", "labelname2id"]], "FastSurferCNN.utils.meters": [[55, 2, 1, "", "Meter"]], "FastSurferCNN.utils.meters.Meter": [[55, 3, 1, "", "disable_confusion_mat"], [55, 3, 1, "", "enable_confusion_mat"], [55, 3, 1, "", "log_epoch"], [55, 3, 1, "", "log_iter"], [55, 3, 1, "", "reset"], [55, 3, 1, "", "update_stats"], [55, 3, 1, "", "write_summary"]], "FastSurferCNN.utils.metrics": [[56, 2, 1, "", "DiceScore"], [56, 1, 1, "", "dice_score"], [56, 1, 1, "", "iou_score"], [56, 1, 1, "", "precision_recall"]], "FastSurferCNN.utils.metrics.DiceScore": [[56, 3, 1, "", "comput_dice_cnf"], [56, 3, 1, "", "compute_dsc"], [56, 3, 1, "", "reset"], [56, 3, 1, "", "update"]], "FastSurferCNN.utils.misc": [[57, 1, 1, "", "check_path"], [57, 1, 1, "", "find_latest_experiment"], [57, 1, 1, "", "plot_confusion_matrix"], [57, 1, 1, "", "plot_predictions"], [57, 1, 1, "", "update_num_steps"]], "FastSurferCNN.utils.parser_defaults": [[58, 2, 1, "", "CanAddArguments"], [58, 2, 1, "", "SubjectDirectoryConfig"], [58, 1, 1, "", "add_arguments"], [58, 1, 1, "", "add_plane_flags"]], "FastSurferCNN.utils.parser_defaults.CanAddArguments": [[58, 3, 1, "", "add_argument"]], "FastSurferCNN.utils.run_tools": [[59, 2, 1, "", "MessageBuffer"], [59, 2, 1, "", "Popen"], [59, 2, 1, "", "PyPopen"]], "FastSurferCNN.utils.run_tools.Popen": [[59, 3, 1, "", "as_future"], [59, 3, 1, "", "finish"]], "FastSurferCNN.utils.threads": [[60, 1, 1, "", "get_num_threads"]], "FastSurferCNN.version": [[61, 2, 1, "", "VersionDict"], [61, 1, 1, "", "filter_git_status"], [61, 1, 1, "", "get_default_version_info"], [61, 1, 1, "", "has_git"], [61, 1, 1, "", "main"], [61, 1, 1, "", "make_parser"], [61, 1, 1, "", "parse_build_file"], [61, 1, 1, "", "print_build_file"], [61, 1, 1, "", "read_and_close_version"], [61, 1, 1, "", "read_version_from_project_file"], [61, 1, 1, "", "section"]], "HypVINN": [[64, 0, 0, "-", "inference"], [66, 0, 0, "-", "run_prediction"]], "HypVINN.data_loader": [[62, 0, 0, "-", "data_utils"], [63, 0, 0, "-", "dataset"]], "HypVINN.data_loader.data_utils": [[62, 1, 1, "", "calculate_flip_orientation"], [62, 1, 1, "", "hypo_map_label2subseg"], [62, 1, 1, "", "hypo_map_prediction_sagittal2full"], [62, 1, 1, "", "hypo_map_subseg_2_fsseg"], [62, 1, 1, "", "reorient_img"], [62, 1, 1, "", "rescale_image"], [62, 1, 1, "", "transform_axial2coronal"], [62, 1, 1, "", "transform_axial2sagittal"]], "HypVINN.data_loader.dataset": [[63, 2, 1, "", "HypVINNDataset"]], "HypVINN.inference": [[64, 2, 1, "", "Inference"]], "HypVINN.inference.Inference": [[64, 3, 1, "", "eval"], [64, 3, 1, "", "get_cfg"], [64, 3, 1, "", "get_device"], [64, 3, 1, "", "get_max_size"], [64, 3, 1, "", "get_model_height"], [64, 3, 1, "", "get_model_width"], [64, 3, 1, "", "get_modelname"], [64, 3, 1, "", "get_num_classes"], [64, 3, 1, "", "get_plane"], [64, 3, 1, "", "load_checkpoint"], [64, 3, 1, "", "run"], [64, 3, 1, "", "set_cfg"], [64, 3, 1, "", "set_model"], [64, 3, 1, "", "setup_model"]], "HypVINN.models": [[65, 0, 0, "-", "networks"]], "HypVINN.models.networks": [[65, 2, 1, "", "HypVINN"], [65, 1, 1, "", "build_model"]], "HypVINN.models.networks.HypVINN": [[65, 3, 1, "", "forward"]], "HypVINN.run_prediction": [[66, 1, 1, "", "get_prediction"], [66, 1, 1, "", "load_volumes"], [66, 1, 1, "", "main"], [66, 1, 1, "", "option_parse"], [66, 1, 1, "", "optional_path"], [66, 1, 1, "", "prepare_checkpoints"], [66, 1, 1, "", "set_up_cfgs"]], "recon_surf": [[67, 0, 0, "-", "N4_bias_correct"], [68, 0, 0, "-", "align_points"], [69, 0, 0, "-", "align_seg"], [70, 0, 0, "-", "create_annotation"], [71, 0, 0, "-", "fs_balabels"], [72, 0, 0, "-", "lta"], [73, 0, 0, "-", "map_surf_label"], [74, 0, 0, "-", "paint_cc_into_pred"], [75, 0, 0, "-", "rewrite_mc_surface"], [76, 0, 0, "-", "rewrite_oriented_surface"], [77, 0, 0, "-", "rotate_sphere"], [78, 0, 0, "-", "sample_parc"], [79, 0, 0, "-", "smooth_aparc"], [80, 0, 0, "-", "spherically_project_wrapper"]], "recon_surf.N4_bias_correct": [[67, 1, 1, "", "get_brain_centroid"], [67, 1, 1, "", "get_image_mean"], [67, 1, 1, "", "get_tal_origin_voxel"], [67, 1, 1, "", "itk_n4_bfcorrection"], [67, 1, 1, "", "normalize_img"], [67, 1, 1, "", "normalize_wm_aseg"], [67, 1, 1, "", "normalize_wm_mask_ball"], [67, 1, 1, "", "options_parse"], [67, 1, 1, "", "read_talairach_xfm"]], "recon_surf.align_points": [[68, 1, 1, "", "angles2rmat"], [68, 1, 1, "", "find_affine"], [68, 1, 1, "", "find_rigid"], [68, 1, 1, "", "find_rotation"], [68, 1, 1, "", "rmat2angles"]], "recon_surf.align_seg": [[69, 1, 1, "", "align_flipped"], [69, 1, 1, "", "align_seg_centroids"], [69, 1, 1, "", "get_seg_centroids"], [69, 1, 1, "", "get_vox2ras"], [69, 1, 1, "", "options_parse"]], "recon_surf.create_annotation": [[70, 1, 1, "", "build_annot"], [70, 1, 1, "", "create_annotation"], [70, 1, 1, "", "map_multiple_labels"], [70, 1, 1, "", "options_parse"], [70, 1, 1, "", "read_colortable"], [70, 1, 1, "", "read_multiple_labels"], [70, 1, 1, "", "write_annot"]], "recon_surf.fs_balabels": [[71, 1, 1, "", "options_parse"], [71, 1, 1, "", "parse_version"], [71, 1, 1, "", "read_colortables"]], "recon_surf.lta": [[72, 1, 1, "", "writeLTA"]], "recon_surf.map_surf_label": [[73, 1, 1, "", "getSurfCorrespondence"], [73, 1, 1, "", "mapSurfLabel"], [73, 1, 1, "", "options_parse"], [73, 1, 1, "", "writeSurfLabel"]], "recon_surf.paint_cc_into_pred": [[74, 1, 1, "", "argument_parse"], [74, 1, 1, "", "paint_in_cc"]], "recon_surf.rewrite_mc_surface": [[75, 1, 1, "", "options_parse"], [75, 1, 1, "", "resafe_surface"]], "recon_surf.rewrite_oriented_surface": [[76, 1, 1, "", "make_parser"], [76, 1, 1, "", "resafe_surface"]], "recon_surf.rotate_sphere": [[77, 1, 1, "", "align_aparc_centroids"], [77, 1, 1, "", "options_parse"]], "recon_surf.sample_parc": [[78, 1, 1, "", "construct_adj_cluster"], [78, 1, 1, "", "find_all_islands"], [78, 1, 1, "", "options_parse"], [78, 1, 1, "", "replace_labels"], [78, 1, 1, "", "sample_img"], [78, 1, 1, "", "sample_nearest_nonzero"], [78, 1, 1, "", "sample_parc"]], "recon_surf.smooth_aparc": [[79, 1, 1, "", "bincount2D_vectorized"], [79, 1, 1, "", "get_adjM"], [79, 1, 1, "", "main"], [79, 1, 1, "", "mode_filter"], [79, 1, 1, "", "options_parse"], [79, 1, 1, "", "smooth_aparc"]], "recon_surf.spherically_project_wrapper": [[80, 1, 1, "", "call"], [80, 1, 1, "", "setup_options"], [80, 1, 1, "", "spherical_wrapper"]]}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "function", "Python function"], "2": ["py", "class", "Python class"], "3": ["py", "method", "Python method"], "4": ["py", "property", "Python property"], "5": ["py", "attribute", "Python attribute"]}, "objtypes": {"0": "py:module", "1": "py:function", "2": "py:class", "3": "py:method", "4": "py:property", "5": "py:attribute"}, "terms": {"": [24, 30, 44, 47, 56, 59, 60, 61, 64, 66, 83, 84, 85, 86, 87, 88, 90, 92, 94, 96, 97, 100, 102, 103, 107, 109, 110, 111], "0": [14, 20, 25, 28, 30, 32, 33, 34, 41, 43, 44, 46, 47, 48, 50, 54, 59, 61, 62, 63, 66, 67, 78, 79, 83, 87, 88, 89, 92, 93, 94, 96, 97, 99, 100, 102, 103, 104, 106, 107, 110, 111], "001": [28, 86, 91, 99, 102, 103], "002": 99, "003": 99, "01": [94, 106], "015": 90, "02": [88, 90, 109], "04": 90, "049": 90, "05": 90, "06": [33, 47], "065": 90, "07": 111, "076": 90, "084": [88, 90, 109], "1": [14, 22, 24, 28, 30, 32, 33, 34, 41, 42, 43, 44, 46, 47, 48, 50, 54, 62, 63, 64, 66, 67, 69, 71, 78, 79, 83, 84, 85, 86, 88, 90, 95, 96, 97, 98, 99, 100, 102, 103, 106, 107, 109, 111], "10": [15, 20, 25, 28, 83, 88, 89, 90, 94, 96, 100, 107, 109, 110, 111], "100": [73, 111], "1000": [28, 34], "101": 100, "1016": [25, 83, 88, 90, 96, 109, 110], "101a": 100, "1024000000": 94, "1030": 103, "10390573": 104, "10390742": 104, "10g": 100, "10min": 100, "11": [89, 94], "110": 67, "11184216": [104, 107], "1162": [83, 88, 96, 107, 109], "117012": [83, 88, 96, 109, 110], "1181": 90, "118933": [83, 88, 96, 109, 110], "1196": 90, "119703": [25, 83, 88, 96, 109], "12": 94, "121": 89, "130": 34, "140": 92, "1402": 90, "140_orig": 92, "1418": 90, "15": 89, "15gb": 89, "16": [32, 86, 87, 89, 100, 106], "172800": 94, "1750814_": 100, "1750814_3": 100, "1750815_": 100, "1750815_1": 100, "1750815_2": 100, "1750815_3": 100, "1750816": 100, "18": 90, "180": 34, "19": [54, 89, 90], "1d": [14, 15], "1e": [33, 47], "1h": 83, "1mm": [33, 34, 46, 83, 88, 96, 103, 110], "1x1x1": [33, 110], "2": [14, 20, 24, 33, 34, 43, 47, 65, 69, 78, 86, 88, 93, 95, 96, 97, 98, 99, 100, 106, 111], "20": [31, 92], "2000": 34, "2004": 97, "2010": 90, "2011": 90, "2012": [88, 90, 109], "2013": 90, "2014": 90, "2016": 94, "2017": 14, "2020": [83, 88, 96, 109, 110], "2022": [25, 54, 83, 88, 96, 109, 110, 111], "2023": [83, 88, 96, 99, 100, 107, 109, 111], "21": [34, 90], "219": [83, 88, 96, 109, 110], "21e31fb5bea5": 104, "21h1": 89, "21h2": 89, "220d": 104, "24": 47, "240min": 100, "249": 90, "251": [83, 88, 96, 109, 110], "255": [33, 62, 67, 86], "256": [33, 42, 65, 105, 106], "256x256x256": [33, 88, 110], "26": 47, "260": 90, "264": [25, 83, 88, 96, 109], "29": 89, "2a3cf0e1a8c5": 104, "2ae5": 104, "2af6da63d5c1414b832c1f606bbd068a": 107, "2d": [15, 41, 42, 79], "2x": 20, "3": [14, 24, 33, 34, 43, 61, 67, 78, 79, 86, 90, 92, 95, 96, 97, 99, 100, 105, 106, 111], "30": [88, 106, 110, 111], "3000": 34, "31": 44, "311": 106, "32": [47, 83, 87, 88, 96, 107, 109, 111], "320": 106, "33": 34, "358": 90, "370": 90, "3d": [33, 34, 45], "3rd": 83, "3t": [86, 87, 88, 90, 94, 98, 100, 110], "4": [43, 44, 67, 68, 71, 78, 84, 86, 88, 90, 94, 95, 97, 99, 100, 102, 103, 107, 109, 111], "40": 92, "4000": 92, "4080": 92, "43": 44, "44": [24, 43], "47b0": 104, "4c83": 104, "4d0e": 104, "5": [15, 24, 34, 43, 47, 83, 90, 92, 95, 96, 97, 103, 105, 107, 110, 111], "50": [34, 67, 97, 105], "5000": 94, "50th": 30, "51": [34, 106], "512000000": 94, "53": 90, "5455": 104, "57": 90, "5t": [88, 98, 110], "5th": 34, "6": [33, 47, 85, 95, 96, 97, 99, 100, 107], "60": [83, 92], "60mm3": 111, "61": [88, 90, 109], "63": 44, "64": [23, 24, 42, 43], "65535": 54, "66": [90, 99], "7": [23, 42, 44, 71, 85, 88, 89, 92, 96, 97, 100, 103, 106, 110], "70": [34, 44], "71": 106, "79": [56, 106], "7mm": [83, 88, 96], "7t": 86, "8": [87, 89, 96, 97, 99, 111], "81": 90, "814d": 104, "853d": 104, "8g": 89, "8gb": [89, 92], "9": [90, 96, 97, 100, 106], "90": 83, "9000": 94, "95": [46, 83, 103, 111], "95mm": 103, "95th": 30, "96": 34, "97": 90, "98mm": 88, "999": [33, 110], "9e0c": 104, "A": [14, 15, 24, 25, 26, 34, 41, 46, 47, 48, 49, 50, 53, 54, 56, 58, 59, 61, 62, 65, 66, 71, 73, 83, 85, 87, 88, 89, 91, 94, 96, 97, 98, 103, 106, 109, 110], "AND": 97, "AS": 97, "AT": 54, "And": [85, 92, 109], "As": [94, 110], "At": 96, "Be": 96, "Being": 84, "But": 96, "By": [14, 30, 56, 59, 86, 88, 94, 99, 102, 103, 107], "FOR": 97, "For": [20, 21, 28, 30, 31, 41, 48, 56, 73, 84, 85, 86, 87, 88, 89, 90, 92, 94, 97, 98, 99, 100, 102, 103, 105, 107, 109, 110, 111], "If": [15, 20, 29, 30, 33, 38, 46, 47, 48, 50, 54, 58, 61, 62, 64, 65, 66, 73, 76, 78, 80, 83, 85, 87, 88, 89, 91, 92, 93, 94, 96, 97, 98, 100, 102, 103, 105, 107, 109, 110, 111], "In": [30, 33, 56, 59, 84, 86, 87, 88, 89, 90, 91, 92, 94, 96, 97, 102, 107, 110], "It": [14, 30, 31, 64, 65, 66, 75, 85, 86, 87, 89, 90, 91, 92, 96, 98, 99, 100, 104, 110], "NOT": [88, 95], "No": [54, 70, 88, 96, 100], "Not": [54, 88, 97, 110], "OF": 97, "OR": [97, 99], "Of": 94, "On": [87, 89, 110], "One": [50, 99, 111], "That": 92, "The": [13, 14, 15, 20, 24, 25, 26, 28, 29, 30, 32, 33, 34, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 54, 57, 58, 59, 61, 62, 63, 64, 65, 66, 67, 68, 70, 71, 73, 78, 80, 81, 83, 84, 85, 86, 87, 88, 89, 90, 91, 94, 96, 97, 98, 99, 100, 102, 103, 106, 107, 110], "Then": 86, "There": [87, 89, 94, 110], "These": [86, 87, 88, 89, 90, 98, 99, 107], "To": [85, 86, 87, 88, 89, 92, 94, 98, 103, 106], "Will": [102, 103, 107, 111], "With": [87, 94, 99, 109, 110], "_": [94, 100], "__arg": 47, "__call": 32, "__call__": [23, 24, 40, 41, 43], "__fn": 50, "__getitem__": 63, "__init__": 46, "__len__": 63, "__pycache__": 61, "_arg": 59, "_arrai": 47, "_arraytyp": 47, "_get_scale_factor": 63, "_globalstat": 47, "_header": 34, "_inttyp": 47, "_numbertyp": 47, "_pad": 32, "_serialexecutor__fn": 50, "_standarized_img": 63, "_t": 50, "_ti": 50, "a423a576": 104, "a_object": 54, "ab": 47, "abil": 28, "abl": [85, 86, 89, 110], "about": [84, 85, 92, 96, 103], "abov": [33, 34, 85, 86, 87, 88, 90, 94, 97, 98, 103, 109], "absolut": [14, 47, 49, 50, 85, 87, 88, 100, 102, 103, 107, 109, 110], "abus": 84, "acceler": 94, "accept": [54, 84, 87, 97, 100, 110], "access": [86, 87, 89, 94, 98], "accord": [21, 34, 53, 73, 89, 92, 99], "accordingli": [21, 31, 85], "account": [33, 84, 85, 86, 92, 94], "accumul": [30, 56, 66], "accur": [83, 88, 90, 96, 109, 110], "accuraci": 96, "achiev": [86, 110], "acknowledg": 95, "acquir": [87, 90, 98], "acquisit": 90, "across": [24, 43, 47, 90, 96, 100], "act": [84, 97], "action": [47, 58, 84, 94], "activ": [16, 43, 61, 88, 89, 99, 102, 103, 107, 109], "actual": [50, 85, 100], "ad": [21, 47, 54, 58, 74, 88, 89, 92, 94], "adam": 106, "adamw": 106, "adapt": [84, 94], "add": [14, 28, 32, 34, 38, 47, 58, 79, 85, 86, 87, 89, 90, 91, 92, 94, 96, 97, 98, 100, 105, 111], "add_argu": [47, 58], "add_background": 54, "add_cereb_wm": 21, "add_measure_pars": 47, "add_plane_flag": 58, "add_text": 47, "add_two_help_messag": 47, "add_usag": 47, "addendum": 97, "addgaussiannois": 32, "addit": [20, 33, 34, 47, 54, 83, 87, 88, 89, 90, 91, 92, 94, 97, 99, 100, 102, 110, 111], "addition": [88, 89, 109, 110], "address": [84, 85, 86, 100], "adefault": 105, "adj": 78, "adjac": [78, 79, 83, 88, 96, 107, 109], "adjaceni": 79, "adjm": 79, "adjust": [28, 33, 66, 87, 92], "admin": 89, "adni": 103, "advanc": [83, 84, 85, 92, 108], "advantag": 90, "advis": [87, 97], "affect": [47, 86, 88, 100], "affin": [13, 14, 21, 33, 34, 47, 60, 66, 68, 69], "affine_info": 34, "after": [13, 24, 42, 43, 47, 54, 59, 61, 87, 89, 90, 91, 92, 94, 96, 98, 99, 100, 103, 106, 110, 111], "afterani": 100, "aftercorr": 100, "ag": [14, 84, 96], "again": [86, 90, 92], "against": [88, 97], "agg": [88, 102, 103, 107], "aggreg": [23, 39, 42, 64, 66, 88, 96, 102, 103, 107, 111], "agnost": 14, "agre": 97, "agreement": [97, 111], "ahmad": 107, "ai": 96, "aim": [85, 99], "al": [14, 25, 83, 88, 90, 96, 109], "algorithm": 111, "alia": 16, "align": [69, 77, 84, 90], "align_aparc_centroid": 77, "align_flip": 69, "align_point": 81, "align_seg": 81, "align_seg_centroid": 69, "all": [14, 15, 18, 20, 30, 34, 46, 47, 50, 54, 59, 61, 66, 70, 71, 78, 79, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 94, 97, 99, 100, 102, 103, 104, 106, 107, 109, 110, 111], "all_col": 71, "all_flag": 58, "all_id": 71, "all_label": 70, "all_merged_label": 47, "all_nam": 71, "all_valu": 70, "alleg": 97, "alloc": [88, 100], "allow": [24, 33, 34, 43, 58, 63, 83, 86, 87, 88, 89, 90, 94, 99, 100, 102, 103, 107], "allow_root": [58, 88, 107], "allows_root": 58, "almost": 87, "alon": 97, "along": [30, 38, 44, 66, 78, 91, 97], "alongsid": 97, "alpha": [39, 68], "alreadi": [30, 33, 34, 38, 47, 54, 56, 85, 86, 87, 88, 89, 90, 94, 102, 103, 105, 107, 110], "also": [15, 21, 28, 44, 47, 54, 58, 61, 65, 70, 73, 85, 86, 87, 88, 89, 90, 91, 92, 94, 96, 98, 99, 100, 103, 107, 109, 110, 111], "alt": 99, "alt_fil": 34, "altern": [34, 47, 83, 86, 87, 90, 100, 102, 103, 106, 110, 111], "alternate_label": 111, "alternate_mean": 111, "alternate_mixing_coeff": 111, "alwai": [33, 47, 50, 61, 85, 88, 94, 96, 102, 103, 110, 111], "am": 85, "amd64": 94, "amdgpu": 94, "among": 86, "amygdala": 96, "an": [13, 14, 15, 20, 25, 28, 33, 34, 47, 48, 49, 50, 54, 56, 58, 61, 65, 66, 67, 70, 72, 78, 79, 84, 86, 87, 88, 89, 90, 91, 92, 94, 96, 97, 99, 106, 107, 110], "analog": 50, "analys": [87, 94, 98], "analysi": [47, 83, 86, 87, 88, 90, 92, 94, 96, 98, 109, 110, 111], "analyz": [33, 34, 46, 86, 87, 90, 102, 103, 110], "anat": [102, 103], "anatom": [34, 83, 90, 91, 110], "anatomi": 90, "angl": 68, "angles2rmat": 68, "ani": [14, 30, 33, 38, 46, 47, 50, 54, 56, 70, 80, 84, 85, 86, 87, 88, 89, 92, 96, 97, 98, 105, 106, 111], "anneal": 28, "annot": [70, 78, 79, 91, 97], "annot_id": 70, "annot_v": 70, "anoth": [54, 70, 85, 86], "answer": 84, "anyth": [102, 103], "apach": [95, 96, 99, 100], "aparc": [34, 38, 58, 69, 77, 79, 86, 87, 88, 91, 92, 96, 102, 103, 105, 110], "aparc_aseg": 103, "aparc_aseg_segfil": [102, 103], "aparc_nam": 38, "aparc_nocc": 38, "aparc_vinn_axial_v2": [103, 104], "aparc_vinn_coronal_v2": 103, "aparc_vinn_sagittal_v2": 103, "aparcdkt": 96, "api": [50, 104], "appear": [84, 97], "append": [34, 70, 71, 87], "appendix": 97, "appl": [88, 94], "appli": [14, 15, 24, 32, 33, 43, 47, 50, 54, 65, 67, 79, 84, 97, 104], "applic": [59, 87, 89, 97], "apply_transform": 14, "apply_warp": [81, 102], "appoint": 84, "approach": [86, 90], "appropri": [84, 89, 97], "approxim": [83, 110], "apt": 89, "ar": [15, 20, 23, 33, 34, 42, 47, 48, 50, 54, 58, 59, 61, 64, 67, 70, 73, 78, 79, 84, 85, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 102, 103, 105, 107, 109, 110], "architectur": [88, 89, 110], "are_all_subject_fil": 50, "area": [65, 91], "arg": [17, 25, 27, 28, 30, 47, 50, 51, 58, 59, 61, 94], "arg_typ": 81, "argpars": [25, 33, 46, 47, 48, 51, 58, 61, 66, 71, 73, 74, 77, 78, 80], "args2cfg": 46, "argument": [25, 27, 33, 34, 38, 46, 47, 48, 50, 51, 58, 61, 66, 80, 87, 91, 94, 95, 98, 99, 100, 110], "argument_pars": 74, "argumentpars": [25, 33, 46, 47, 58, 61, 66], "argumenttypeerror": 48, "aris": 97, "arithmet": [30, 56], "arm": [85, 89], "around": [33, 47, 67, 73, 78, 83, 96], "arr": 20, "arrai": [13, 14, 15, 20, 29, 33, 34, 44, 45, 47, 54, 56, 62, 72, 73, 74, 78, 79, 100], "array_lik": [14, 30, 47], "array_or_tensor": 54, "arraylik": [67, 70, 72, 74, 77, 79], "artefact": 96, "artifact": 14, "as_futur": 59, "asd": 30, "aseg": [16, 21, 34, 35, 38, 58, 67, 69, 74, 86, 87, 88, 91, 92, 96, 102, 103, 105, 110, 111], "aseg_cc": 74, "aseg_data": 45, "aseg_map": 15, "aseg_nam": 103, "aseg_nocc": [34, 103], "asegdkt": [74, 83, 86, 88, 91], "asegdkt_segfil": [44, 50, 83, 87, 88, 95, 102, 103, 110], "ask": [85, 89], "assd": 30, "assert": 97, "assert_no_root": 50, "assertionerror": [65, 66], "assess": 91, "assign": [50, 87, 90, 99, 100], "associ": [14, 40, 47, 50, 54, 61, 97, 100], "assum": [33, 47, 58, 68, 89, 97, 110], "asymmetri": 90, "async_finish": 59, "async_io": [22, 46, 64, 66, 102, 103, 107], "async_save_img": 46, "asynchron": [46, 50, 66, 102, 103, 107], "aten": 89, "atla": [87, 88, 91, 96, 98, 110], "atlas": 110, "atrophi": 90, "attach": 97, "attack": 84, "attent": [77, 84], "attest": 95, "attr_nam": 50, "attribut": [16, 22, 28, 32, 38, 39, 40, 41, 42, 43, 46, 50, 54, 56, 58, 59, 61, 64, 65, 95, 97], "attributeerror": 50, "aug": [54, 106], "augment": [16, 35, 81, 106], "augmentationpadimag": 32, "augmentationrandomcrop": 32, "author": [54, 97, 99, 100, 102, 111], "authorship": 97, "auto": [22, 46, 48, 50, 64, 66, 86, 87, 88, 102, 103, 107, 111], "auto_noccseg": [86, 87, 91, 92, 103, 105], "autodetect": 88, "autom": [83, 88, 96, 107, 109], "automat": [33, 63, 66, 86, 87, 88, 91, 94, 98, 99, 104, 110, 111], "aux_subjects_fil": 19, "auxiliari": 19, "avail": [30, 56, 60, 66, 84, 86, 87, 89, 91, 94, 97, 98, 102, 106, 107, 110], "available_s": 38, "averag": 30, "avoid": [86, 87, 88, 90, 94, 98, 110], "awar": [85, 96, 110], "ax": [30, 62], "axi": [15, 34, 38, 62], "axial": [15, 34, 38, 39, 46, 62, 66, 102, 103, 105, 106, 107], "axial2coron": [15, 62], "axial2sagitt": [15, 62], "aziz": [83, 88, 96, 107, 109], "b": [34, 54, 59, 83, 85, 87, 88, 89, 90, 92, 96, 97, 98, 99, 100, 105, 107, 109, 110], "b2share": [104, 107], "b5b32d45fc59": 104, "bach": 55, "back": [15, 34, 62, 77, 89, 92], "backbon": 46, "background": [14, 29, 30, 44, 67, 106], "bahrami": [25, 83, 88, 96, 107, 109], "balanc": [15, 34], "ball": [67, 78], "ban": 84, "bar": [94, 99], "base": [13, 14, 23, 25, 30, 47, 50, 54, 62, 63, 66, 69, 83, 85, 86, 87, 88, 89, 90, 91, 94, 96, 97, 99, 100, 102, 103, 104, 106, 109, 110, 111], "base_lr": [28, 106], "base_ornt": 62, "base_r": 106, "base_shap": 20, "baseexcept": 50, "baseid": [88, 110], "bash": [89, 94, 100], "bashrc": 89, "basi": [97, 110], "basic": [87, 94], "batch": [15, 22, 24, 29, 39, 40, 42, 43, 46, 57, 66, 88, 96, 100, 102, 103, 106, 107, 108], "batch_dict": 31, "batch_loss": 55, "batch_output": [31, 57], "batch_siz": [39, 46, 65, 66, 88, 102, 103, 106, 107], "bbox": 16, "bbox_3d": 34, "bctx": 94, "becaus": [94, 100, 111], "been": [85, 89, 97], "befor": [59, 86, 94, 98, 99], "beforehand": 88, "behalf": 97, "behavior": [59, 84, 85, 86, 103], "behind": 95, "being": [14, 47, 54, 93, 99], "belong": [47, 87], "below": [33, 34, 86, 87, 88, 89, 91, 92, 97, 103, 105, 110], "benefici": 97, "benefit": [87, 96, 99], "bernal": 90, "bert": 90, "bert_1": 90, "bert_2": 90, "best": [26, 49, 84, 95, 110], "best_metr": [26, 49], "beta": 68, "better": [87, 88, 89, 107, 110], "between": [14, 30, 33, 34, 38, 44, 47, 48, 54, 68, 79, 88, 90, 103], "beyond": 83, "bg_intersect": 44, "bg_label": 44, "bia": [14, 47, 67, 83, 88, 90, 92, 95, 102, 107, 109, 110], "bias_correct": 86, "biasfield": [86, 87, 88, 91, 111], "bicub": 65, "bid": [102, 103], "bigger": [44, 48, 88], "biject": 54, "bilinear": 65, "bill": 94, "billot": 14, "bin": [48, 89], "binar": 78, "binari": [21, 30, 34, 47, 67, 89, 107], "bincount2d_vector": 79, "bind": 97, "biomed": 30, "bit": 92, "bkg": 34, "blank": [15, 20, 34, 38, 61], "blank_slice_thresh": 105, "bleed": [94, 98], "block": [23, 24, 42, 43, 59, 65], "blt": 38, "blue": [31, 57], "blur_factor": 14, "bn": [24, 43], "bn0": 43, "bodi": 84, "bonu": 92, "bool": [15, 19, 26, 33, 34, 38, 39, 44, 47, 49, 50, 54, 56, 61, 62, 66, 69, 70, 71, 76, 79], "boolean": 15, "bootstrap": 94, "border": [20, 38, 47, 105], "border_patch": 47, "both": [13, 47, 56, 64, 84, 88, 89, 90, 94, 99, 100, 107, 109], "bottleneck": 42, "bottom_left": 65, "bottom_right": 65, "bound": [20, 34], "boundari": [15, 78, 79, 111], "bounding_volume_offset": 20, "box": 34, "br": [47, 111], "brain": [14, 46, 67, 83, 86, 87, 88, 89, 91, 92, 96, 103, 107, 109, 110], "brain_seg": 16, "brainmask": [86, 88, 91, 92, 103, 110], "brainmask_nam": [58, 103], "brainseg": 111, "brainsegnotv": 111, "brainsegnotventsurf": 111, "brainsegvol": 111, "brainstem": [21, 96], "brainvol": 111, "brainvolstat": 47, "branch": [61, 85, 87, 88, 89], "break": [47, 89], "bretel": [83, 88, 96, 107, 109], "brew": 89, "broken": [87, 89], "brun_fastsurf": [87, 90, 100, 108, 110], "brun_subject": 87, "buckner_data": 92, "budget": 100, "buffer": 39, "bug": 95, "build": [23, 28, 42, 61, 65, 70, 83, 87, 88, 89, 92, 95, 96, 109, 110], "build_annot": 70, "build_cach": 61, "build_fil": 61, "build_model": [23, 42, 65], "builder": 94, "buildkitd": 94, "buildx": 94, "built": [89, 94], "builtin": [50, 99], "bundl": 89, "byte": 50, "c": [33, 41, 42, 43, 83, 89, 97], "c6cf7bc6": 104, "ca": [89, 94], "cach": 61, "cachemount": 94, "calcul": [26, 30, 41, 46, 47, 49, 56, 83, 88, 102, 111], "calculate_flip_orient": 62, "calculate_merged_label": 47, "call": [32, 58, 80, 87, 89, 90, 92, 98, 100, 102, 103, 106, 107, 110], "callabl": [30, 50, 56, 58], "callosum": [34, 38, 74, 87, 91, 92, 105], "can": [14, 20, 30, 33, 34, 41, 44, 48, 50, 54, 56, 58, 61, 65, 66, 70, 73, 78, 79, 85, 87, 88, 89, 90, 92, 93, 94, 95, 96, 98, 99, 100, 102, 103, 104, 106, 107, 110, 111], "can_resolve_attribut": 50, "can_resolve_filenam": 50, "canaddargu": 58, "candid": 21, "candidate_lbl": 21, "cannot": [94, 97, 99, 111], "cap": [34, 89], "capabl": 99, "care": [70, 87, 94], "carefulli": [85, 86], "carol": 14, "carri": 97, "case": [25, 30, 33, 56, 59, 71, 73, 85, 86, 87, 88, 89, 92, 94, 96, 98, 99, 100, 110], "case_bias_correct": 86, "case_bias_onli": 86, "case_with_edit": 86, "cast": 39, "catch": 46, "categor": 56, "caus": [50, 66, 86, 94, 97, 98], "cc": [74, 86], "ccomput": 24, "cd": [85, 87, 89, 92, 98, 100], "ce": 41, "cell": 92, "center": [20, 65, 67], "centroid": [67, 69, 77], "centroids_dst": 69, "centroids_mov": 69, "cereb": [21, 83], "cereb_segfil": [88, 102], "cereb_statsfil": 102, "cereb_subseg": [15, 20, 21], "cereb_subseg_lateral_mask": 21, "cerebdataset": 16, "cerebellar": [21, 83, 102], "cerebellum": [15, 25, 83, 88, 91, 92, 96, 102, 109], "cerebnet": [81, 83, 88, 89, 95, 96, 101, 104, 108, 109], "cerebnet_axial_v1": 102, "cerebnet_coronal_v1": 102, "cerebnet_model": 81, "cerebnet_sagittal_v1": 102, "cerebnetdataset": 18, "cerebr": 34, "cerebralwhitematt": 111, "cert": 94, "certain": [102, 103, 107, 110, 111], "certif": [89, 94], "cfg": [14, 16, 17, 18, 19, 22, 26, 28, 29, 31, 35, 36, 39, 41, 42, 46, 49, 53, 55, 57, 63, 64, 65, 66, 106], "cfg_": 58, "cfg_ax": [46, 66, 103, 107], "cfg_cor": [46, 66, 103, 107], "cfg_file": [46, 51, 106], "cfg_sag": [46, 66, 103, 107], "cfgnode": [26, 31, 36, 39, 41, 42, 46, 49, 51, 53, 57, 64, 65, 66], "chain": 54, "challeng": 30, "chan": [83, 96], "chang": [54, 81, 85, 86, 87, 88, 89, 90, 94, 97, 98, 103, 106, 109, 110, 111], "channel": [15, 40, 106], "charact": [47, 97], "characterist": 84, "charg": 97, "check": [26, 33, 34, 44, 47, 48, 49, 50, 54, 66, 85, 86, 88, 89, 96, 100, 102, 103, 104, 107, 110], "check_affine_in_nifti": 33, "check_and_download_ckpt": 49, "check_dtyp": 33, "check_path": 57, "check_shape_affin": 47, "check_volum": 44, "checkout": [85, 94], "checkpoint": [39, 46, 58, 61, 64, 66, 81, 88, 89, 100, 102, 104], "checkpoint_dir": [26, 49], "checkpoint_nam": 49, "checkpoint_path": [26, 49], "checkpointconfigdict": 49, "chiasma": 34, "chip": [88, 89, 94], "chmod": 89, "choic": [88, 105, 107, 109, 111], "choos": [97, 103], "choroid": 44, "chosen": 86, "chunk": 50, "chunksiz": 50, "circumst": 84, "cite": [83, 88, 96, 107, 109, 110], "ckpt": [39, 46, 49, 64, 107], "ckpt_": 58, "ckpt_ax": [46, 66, 102, 103, 107], "ckpt_cor": [46, 66, 102, 103, 107], "ckpt_dir": [26, 49], "ckpt_sag": [46, 66, 102, 103, 107], "claim": 97, "clarifi": 84, "class": [14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 46, 47, 49, 50, 54, 55, 56, 57, 58, 59, 61, 63, 64, 65, 81, 83, 106], "class_id": 30, "class_idx": 30, "class_list": 14, "class_nam": [29, 55], "class_wise_weight": 15, "classes_list": 14, "classif": [24, 42, 43], "classifi": [24, 26, 42, 43, 49, 65], "classifierblock": [24, 43, 65], "classmethod": 54, "classname_to_id": 29, "clean": [34, 103], "clean_cortex_label": 34, "cleanup": [87, 100], "clear": [85, 96], "cli": 94, "clinic": 96, "clone": [85, 87, 89], "close": [34, 61], "closest": [34, 73, 78], "cloud": 92, "cluster": [95, 100, 110], "cm": [31, 56, 57], "cmap": [31, 57], "cmax": 34, "cmdf": 85, "cmin": 34, "cmp_dtype": 47, "cnf": 56, "cnf_mat": 56, "cnn": [42, 87], "co": [83, 85, 88, 91, 96, 107, 109, 110], "code": [34, 47, 59, 80, 89, 95, 97, 100, 103, 106, 107], "code_1": 80, "coeffici": [30, 56, 111], "col": 70, "col_id": 70, "colab": 95, "colappend": 71, "collab": 92, "collect": 85, "colnam": 71, "colon": [87, 94, 98, 110], "color": [31, 34, 38, 54, 57, 70, 71, 78, 103, 105], "color_palett": 54, "colorlookupt": 54, "colorlut": [34, 47], "colormap": [54, 92], "colormapregistri": 57, "colort": [70, 71], "colortab": 70, "colortab_nam": 70, "colour": [57, 70], "column": [47, 105], "com": [14, 85, 87, 89, 90, 94], "combi": [34, 105], "combin": [24, 28, 34, 41, 43, 70, 88, 90, 97, 105, 111], "combinedloss": 41, "come": [87, 92], "comma": [47, 100], "command": [25, 33, 44, 45, 47, 61, 66, 67, 69, 70, 71, 73, 74, 75, 76, 77, 78, 79, 80, 85, 86, 87, 88, 89, 90, 92, 94, 98, 99, 109, 110, 112], "command1": 80, "command2": 80, "commandlin": [47, 89, 112], "comment": [84, 85], "commerci": 97, "commit": [84, 85], "common": [81, 84, 97, 102, 103, 107], "commonli": 30, "commun": [84, 85, 86, 97], "compar": [30, 33, 86, 90, 96, 107], "compat": [47, 66, 83, 96, 100, 111], "competit": [23, 24, 42, 43], "competitivedecoderblock": [24, 43], "competitivedenseblock": [24, 43], "competitivedenseblockinput": [24, 43], "competitivedensedecod": [24, 43], "competitiveencoderblock": [24, 43], "competitiveencoderblockinput": [24, 43], "compil": [85, 97], "complaint": 84, "complet": [34, 80, 85, 88], "compli": [88, 97], "compon": [16, 21, 30, 34, 56, 78, 85, 89, 103], "compress_out_spac": 54, "compris": [24, 43, 86], "comput": [14, 23, 24, 29, 30, 33, 39, 44, 47, 56, 62, 64, 67, 78, 85, 86, 87, 92, 94, 96, 97, 98, 110, 111], "comput_dice_cnf": 56, "compute_dsc": 56, "concaten": 61, "concatenation": [23, 42], "concern": 91, "concurr": [34, 46, 47, 59], "conda": 61, "condit": [33, 97, 111], "conduct": 95, "conf": 88, "conf_nam": [50, 58, 102, 103], "confidenti": 84, "config": [26, 28, 31, 36, 39, 41, 42, 46, 49, 51, 53, 57, 58, 64, 65, 66, 94, 102, 105, 106, 107], "config_fil": 27, "configtyp": [49, 58], "configur": [25, 26, 31, 36, 39, 41, 46, 47, 49, 51, 53, 57, 64, 65, 66, 85, 94, 97, 106, 111], "conflict": [85, 89, 94], "conform": [34, 46, 50, 81, 86, 87, 88, 91, 102, 103, 110], "conform_and_save_orig": 46, "conform_min": 34, "conform_to_1mm_threshold": [33, 46, 103], "conform_vox_s": 33, "conformed_img_s": 33, "conformed_nam": [87, 88, 102, 103], "conformed_t1_fil": 50, "conformed_t1_output": 110, "conformed_vox_s": 33, "confus": [29, 31, 55, 56, 57], "conjeti": [83, 88, 96, 109, 110], "connect": [16, 23, 24, 30, 34, 42, 43, 47], "consecut": 54, "consequenti": 97, "consid": [14, 30, 33, 47, 70, 78, 81, 84, 85, 86, 88, 100, 102, 103, 107], "consist": [24, 83, 88, 89, 90, 97], "consol": [87, 99, 110], "conspicu": 97, "constitut": 97, "constrain": [47, 90], "constru": 97, "construct": [46, 84, 90, 100], "construct_adj_clust": 78, "constructor": 80, "contact": 84, "contain": [14, 15, 20, 29, 30, 34, 39, 41, 44, 47, 50, 54, 56, 57, 58, 59, 61, 64, 65, 66, 70, 78, 83, 87, 88, 89, 90, 91, 92, 94, 97, 98, 99, 100, 103, 106, 110], "containerd": 94, "content": [49, 59, 61, 97], "context": [85, 94], "continu": [15, 70, 85, 89], "continuum": 89, "contract": 97, "contrari": 103, "contrast": 14, "contribut": [14, 84, 86, 93, 95, 97], "contributor": [95, 96, 97], "contributori": 97, "control": [86, 87, 88, 92, 97, 99, 107, 110], "conv": [24, 43], "conv0": 43, "conv1": 43, "conv2": 43, "conv3": 43, "conveni": [59, 86, 92], "convent": 50, "converg": 67, "convers": [97, 98], "convert": [14, 30, 32, 34, 47, 48, 54, 66, 68, 92, 98], "convinc": 85, "convolut": [23, 24, 42, 43, 106], "coord": [69, 73], "coordin": [19, 34, 67, 73, 78], "copi": [50, 74, 86, 92, 97, 100], "copy_orig_nam": 50, "copy_orig_t1_fil": 50, "copyright": 97, "core": [83, 87, 88, 99], "coreg": [66, 88, 107], "corner": 47, "coron": [15, 34, 39, 46, 62, 66, 102, 103, 105, 106, 107], "coronal2axi": [15, 34], "coronal2sagitt": [15, 34], "corpu": [34, 38, 74, 87, 91, 92, 105], "correct": [21, 34, 35, 47, 63, 67, 73, 75, 76, 83, 84, 87, 88, 89, 90, 91, 92, 95, 96, 102, 103, 107, 109, 110, 111], "correct_cereb_brainstem": 21, "correctli": [33, 75, 92, 94], "correspond": [13, 14, 15, 24, 34, 43, 44, 50, 54, 66, 70, 73, 78, 79, 86, 88, 90, 91, 96, 110], "cortex": [34, 38, 70, 78, 79, 86, 91, 105, 110, 111], "cortex_border_mask": 34, "cortex_label_nam": 70, "cortex_mask": 34, "cortex_stop": 34, "cortic": [34, 69, 78, 83, 86, 90, 91, 92, 96, 110], "cosin": 28, "cosineannealingwarmrestart": 53, "cosineannealingwarmrestartsdecai": 28, "cosinelr": 28, "cosinewarmrestart": 106, "could": [84, 87, 89], "count": [47, 60, 79, 87], "counterclaim": 97, "coupl": [89, 92], "cours": 90, "coven": 95, "cover": [33, 85, 92], "cpu": [50, 60, 87, 88, 92, 96, 98, 99, 100, 102, 103, 107, 110, 111], "cpu_onli": 100, "cpu_partit": 87, "cr": 86, "creat": [15, 17, 21, 26, 33, 34, 36, 38, 45, 46, 47, 49, 50, 54, 57, 66, 70, 71, 73, 74, 75, 76, 77, 78, 79, 80, 84, 85, 87, 88, 89, 90, 91, 92, 94, 96, 98, 99, 102, 103, 107, 109, 110, 111], "create_annot": 81, "create_checkpoint_dir": [26, 49], "create_hdf5_dataset": [18, 38], "create_mask": 45, "create_weight_mask": 34, "create_weight_mask2d": 15, "creation": [87, 88, 89, 95, 105, 107, 110], "criteria": 33, "critic": [84, 85], "crop": [13, 20, 32, 33, 40, 42, 47, 65], "crop_patch_to_mask": 47, "crop_posit": [40, 42, 65], "crop_transform": 20, "crop_typ": 32, "cross": [23, 41, 42, 55, 78, 88, 90, 97, 110], "cross_entropy_loss": 41, "crossentropi": 41, "crossentropy2d": 41, "csc_matrix": 78, "csf": 34, "csr": 79, "csr_matrix": 79, "csv": [100, 102, 103, 105], "csv_file": [58, 102, 103, 105], "ctrl": 99, "ctx": [34, 105], "ctx_thresh": 34, "cube": [33, 75, 88], "cubic": [33, 34], "cuda": [30, 43, 50, 56, 88, 89, 94, 99, 102, 103, 107, 111], "cur_epoch": [26, 28, 29, 55], "cur_it": [29, 55], "curl": [89, 92], "curr_it": 28, "current": [26, 28, 29, 46, 47, 49, 50, 54, 55, 70, 85, 88, 93, 94, 98, 100, 102], "current_plan": 46, "current_subject": 19, "curv": 91, "curvatur": 91, "custom": [89, 94, 98, 110], "custom_config": 106, "customari": 97, "cwd": [98, 99], "cyclic": 90, "d": [25, 83, 85, 87, 88, 94, 96, 97, 99, 109, 110], "d9e37247": 104, "d_1": 20, "d_2": 20, "d_n": 20, "daemon": [94, 98], "damag": [96, 97], "dat": 86, "data": [13, 15, 17, 19, 20, 21, 22, 28, 30, 33, 34, 36, 39, 40, 42, 43, 45, 46, 47, 48, 54, 57, 58, 62, 63, 64, 66, 75, 78, 86, 87, 88, 89, 91, 92, 94, 95, 96, 98, 99, 100, 103, 105, 107, 110, 112], "data2": 34, "data_cfg": 16, "data_dict": [15, 20], "data_dir": 105, "data_inseg": 45, "data_load": [38, 57, 81, 105, 110], "data_path": 38, "data_set_s": 38, "data_util": 81, "datadir": [87, 110], "datafram": [34, 38, 47, 54], "dataload": [17, 36, 39, 57, 64, 81, 106], "dataset": [14, 17, 36, 38, 64, 81, 86, 89, 94, 105, 106], "dataset_nam": [18, 38], "dataset_path": [16, 35], "datatyp": 48, "datautil": 34, "date": [54, 71, 87, 97, 99, 100, 111], "david": [54, 99, 100, 107, 111], "de": [34, 84, 99, 100, 104, 107], "deactiv": [83, 88, 107], "debug": [47, 87, 99, 108], "dec": 111, "decai": 28, "decay_base_lr": 28, "decid": 89, "decis": [88, 96, 102, 103, 107], "decod": [24, 42, 43], "decode1": 42, "decode2": 42, "decode3": 42, "decode4": 42, "decoder_output1": 42, "dedic": [90, 96, 110], "deem": 84, "deep": [25, 34, 58, 74, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 96, 99, 100, 102, 103, 107, 109, 110], "deep_sulci_and_wm_strand_mask": 34, "deepmi": [87, 89, 92, 94, 98, 110], "default": [14, 15, 19, 20, 26, 28, 30, 31, 33, 34, 38, 39, 41, 42, 44, 46, 47, 49, 50, 54, 55, 56, 57, 58, 59, 60, 61, 62, 64, 65, 66, 67, 69, 70, 71, 73, 77, 78, 79, 83, 86, 87, 88, 89, 94, 96, 98, 100, 102, 103, 104, 105, 109, 110, 111, 112], "default_criteria": 33, "default_devic": 39, "defaults_path": 58, "defend": 97, "defin": [20, 24, 30, 34, 43, 44, 47, 50, 56, 64, 79, 84, 86, 87, 88, 90, 94, 97, 99, 100, 102, 103, 106, 107, 110, 111], "definit": [23, 42, 88, 91, 97, 102, 103], "deform": 102, "degre": 68, "deleg": 99, "delet": 85, "deliber": 97, "delimit": [87, 100], "delin": 83, "delta": 86, "dens": [23, 24, 42, 43], "depend": [61, 85, 86, 87, 93, 94, 100, 110, 111], "depth": 13, "deriv": [20, 86, 88, 96, 97], "derogatori": 84, "describ": [25, 47, 58, 61, 66, 85, 89, 90, 92, 97], "descript": [85, 91, 93], "descriptor": 48, "design": 97, "desir": [34, 39, 44, 50], "desktop": [89, 94], "dest": 58, "destin": [68, 72, 77, 79], "detach": 94, "detail": [25, 28, 33, 47, 83, 84, 85, 86, 87, 88, 89, 92, 94, 96, 109], "detect": [50, 86, 87, 88, 90, 94, 99], "determin": [28, 30, 33, 34, 60, 61, 62, 63, 70, 79, 84, 85, 88, 94, 97, 103], "deubg": 31, "dev": [85, 87, 88, 89, 94, 110], "develop": [81, 85, 87, 94, 96, 110], "deviat": [14, 32, 33], "devic": [22, 29, 30, 39, 43, 46, 50, 55, 56, 58, 64, 66, 87, 88, 89, 94, 96, 99, 102, 103, 107, 111], "device_num": [88, 103], "dice": [23, 29, 30, 41, 42, 55, 56], "dice_loss": 41, "dice_scor": [29, 30, 56], "diceloss": 41, "dicescor": [30, 56], "dict": [15, 16, 19, 20, 29, 38, 39, 43, 44, 46, 47, 49, 50, 54, 58, 63, 72], "dictionari": [15, 19, 20, 29, 34, 38, 44, 47, 49, 54, 58, 61, 64, 66], "did": [94, 100, 110], "dier": [83, 88, 90, 96, 109, 110], "dieseas": 96, "differ": [33, 39, 50, 66, 84, 86, 87, 88, 89, 90, 94, 96, 97, 99, 109, 110, 111], "digit": [47, 94, 111], "dilat": [34, 44, 45, 103], "dilshad": 107, "dim": 20, "dimens": [13, 15, 20, 30, 33, 42, 66, 106, 110], "dimension": [20, 34, 40, 67], "dir": [26, 49, 61, 70, 88, 99, 107, 109, 110], "direct": [15, 33, 62, 78, 86, 88, 89, 90, 97, 98, 102, 107], "directli": [87, 88, 94, 96, 99, 102, 103, 107, 110, 111], "director": 70, "directori": [13, 18, 26, 38, 46, 47, 49, 50, 58, 61, 66, 70, 85, 86, 87, 88, 89, 90, 91, 92, 94, 98, 100, 102, 105, 106, 107, 109, 110, 111], "disabl": [55, 84, 88, 99, 110], "disable_confusion_mat": 55, "discard": 105, "disclaim": 97, "disconnect": [21, 45, 78], "disconnetct": 78, "discourag": [87, 94], "discriminator_block": 24, "discuss": 97, "diseas": 90, "disk": 73, "displai": [33, 92, 97], "distanc": [30, 73, 78], "distort": 86, "distribut": [30, 34, 39, 56, 87, 89, 97, 100], "distro": 89, "div": 47, "diverg": 85, "divid": 47, "divis": 92, "dkm": 94, "dkt": [69, 74, 87, 88, 91, 96, 110], "dktatla": [34, 58, 83, 86, 87, 88, 91, 92, 102, 103, 105, 110], "dl": [88, 102, 103, 110], "dnum": 45, "do": [33, 38, 47, 66, 84, 87, 88, 89, 90, 92, 94, 95, 97, 98, 100, 102, 103, 105, 107, 109, 110, 111], "doc": [28, 89, 94], "docker": [90, 95, 96, 98, 99], "docker_buildkit": 94, "dockerfil": 94, "dockerhub": [87, 89, 95, 98, 110], "document": [28, 61, 85, 87, 89, 91, 94, 96, 97, 99, 100, 109], "doe": [20, 33, 34, 47, 49, 58, 61, 74, 87, 88, 90, 94, 96, 97, 99, 100, 102, 103, 107, 110, 111], "doesn": 14, "doi": [25, 83, 88, 90, 96, 107, 109, 110], "don": [89, 92, 110], "done": [33, 62, 88, 89, 90, 99, 100, 102, 103, 107], "dot": 111, "doubl": 100, "down": 96, "download": [49, 66, 89, 92, 94, 104], "download_checkpoint": [49, 81, 89, 108, 112], "downsampl": 42, "downstream": [86, 90, 91, 95], "draw": 50, "dri": [89, 94], "driver": [89, 94], "drop": [21, 26, 34, 49, 71, 87, 110, 111], "drop_classifi": [26, 49], "drop_disconnected_compon": 21, "drop_unknown": 71, "drug": 90, "dry": [87, 100], "dry_run": [59, 94], "dsc": 56, "dst": 69, "dst_fname": 72, "dst_header": 72, "dst_max": 33, "dst_min": 33, "dtype": [15, 33, 34, 46, 48], "dtypelik": [34, 47], "due": [89, 96], "dummi": 50, "dura": 86, "dure": [14, 55, 63, 86, 89, 104, 106, 109], "dx": [83, 88, 96, 109, 110], "dzne": [84, 94, 99, 100, 107], "dzne_manu": 21, "e": [21, 25, 30, 33, 34, 47, 48, 50, 56, 61, 69, 70, 73, 75, 83, 84, 85, 86, 87, 88, 90, 91, 93, 94, 96, 98, 99, 100, 102, 103, 104, 105, 107, 109, 110, 111], "each": [14, 15, 20, 21, 29, 30, 34, 42, 45, 47, 56, 58, 66, 73, 78, 79, 88, 90, 97, 99, 100, 109, 110], "earli": 90, "earlier": 91, "easili": [89, 98], "echo": [89, 100], "edg": [15, 32, 34, 38, 78, 79, 105], "edge_w": 105, "edge_weight": 38, "edit": [84, 88, 89, 94, 95, 110], "editori": 97, "edu": [86, 87, 88, 92, 98, 110], "educ": [83, 84, 96], "effect": [34, 47, 54, 83, 90, 95, 111], "effici": [20, 47, 89, 94, 100], "either": [20, 32, 33, 34, 39, 41, 47, 49, 59, 61, 73, 85, 90, 92, 97, 100, 103, 111], "elabor": 97, "electron": [84, 97], "element": [15, 20, 29, 30, 34, 38, 50, 66, 78, 102, 103, 105, 107, 111], "els": [20, 30, 76, 85, 102, 103, 107], "emad": 107, "email": [89, 100, 102], "empathi": 84, "emphas": 15, "emploi": 83, "empti": [47, 54, 61, 78, 87, 88, 94, 98, 100, 111], "emul": 89, "en": 94, "enabl": [14, 55, 88, 89, 96, 99, 102, 106, 107, 110], "enable_confusion_mat": 55, "encod": [24, 42, 43], "encode1": 42, "encode2": 42, "encode3": 42, "encode4": 42, "encourag": [85, 90], "end": [24, 29, 33, 43, 47, 79, 86, 87, 99, 100], "end_sect": 47, "enforc": [33, 90, 95], "engin": [30, 56], "enhanc": 95, "enough": [88, 89, 90, 102, 103, 107, 110], "ensur": [85, 110], "entir": 107, "entiti": 97, "entri": [34, 47, 50, 54, 58, 61, 90, 94], "entropi": [23, 41, 42, 55], "entrypoint": [87, 94, 110], "enum": [33, 45], "enumer": [33, 86], "env": [88, 89, 99, 109, 110], "environ": [84, 85, 87, 88, 94, 98, 99, 109], "ep": [33, 47], "epoch": [26, 28, 29, 49, 55, 106], "epsilon": [33, 47], "equal": [30, 47, 48, 64, 70, 78, 88], "equival": [33, 87, 88, 91, 98, 102, 103, 107, 110, 111], "erod": [34, 103], "eros": [34, 45], "err": 59, "err_str": 59, "error": [34, 47, 50, 61, 66, 75, 85, 86, 96], "especi": [86, 87], "estim": [14, 44, 86, 87, 88, 90, 91, 92, 96, 109, 110], "estimatedtotalintracranialvol": 111, "estrada": [83, 88, 96, 107, 109, 110], "et": [14, 25, 83, 88, 90, 96, 109], "eta_min": 28, "etc": [47, 50, 88, 90, 93, 94, 96, 100, 110, 111], "ethnic": 84, "etiv": [86, 87, 88, 110, 111], "eudat": 107, "eval": [19, 39, 64], "evalu": [14, 39, 47, 64, 102, 107, 111], "even": [86, 87, 89, 90, 97], "event": [84, 90, 97], "everi": 89, "everyon": 84, "everyth": 89, "everywher": 30, "evolv": 90, "exact": 111, "exactli": [33, 47], "exampl": [30, 34, 56, 78, 84, 86, 88, 89, 90, 92, 95, 96, 97, 98, 99, 100, 107, 111, 112], "except": [25, 46, 50, 87, 90, 94, 97, 99, 109], "excit": 96, "exclud": [47, 61, 86, 87, 89, 97, 98, 111], "exclude_id": 47, "excludeid": 111, "exclus": [79, 97, 111], "exec": [87, 90, 92, 94, 98, 99, 100, 110], "execut": [25, 50, 58, 87, 88, 92, 94, 97, 98, 99], "executor": [46, 47, 50, 59], "exercis": 97, "exist": [26, 33, 47, 49, 50, 54, 66, 70, 85, 86, 87, 88, 90, 94, 98, 102, 103, 105, 107, 110, 111], "exit": [88, 100], "expand": 54, "expect": [29, 30, 47, 56, 84, 85, 86, 93, 99, 100, 111], "experi": [26, 31, 49, 57, 84, 92], "experienc": [85, 95], "experiment": [83, 88, 90, 103], "expert": [88, 95, 110], "explain": [85, 89, 94], "explicit": 84, "explicitli": [34, 47, 88, 97, 111], "export": [86, 87, 88, 89, 90, 109, 110], "expr_dir": [26, 49], "expr_num": [26, 31, 49], "express": [84, 97], "ext": 88, "extend": [28, 54, 65, 86, 92], "extens": [59, 71, 98], "exterior": 34, "extern": [86, 88, 100, 107], "extra": 100, "extra_head": 47, "extra_singularity_opt": 100, "extra_singularity_options_seg": 100, "extra_singularity_options_surf": 100, "extract": [33, 34, 46, 47, 58, 61, 68, 69, 86, 90, 96], "exvivo": 70, "f": [70, 73, 78, 85, 88, 89, 90, 98, 110], "f_high": 33, "f_low": 33, "faber": [25, 83, 88, 96, 109], "face": [47, 84], "fact": 111, "factor": [28, 33, 38, 39, 42, 47, 63, 64, 65, 67], "fail": [34, 80, 86, 88, 89, 99, 100, 102, 103, 107], "failur": [25, 60, 66, 97, 100], "fair": 84, "faith": 84, "fall": 89, "fallback": [80, 89], "fals": [15, 18, 19, 20, 22, 24, 26, 30, 33, 34, 35, 43, 46, 47, 49, 54, 56, 61, 62, 64, 66, 69, 102, 103, 104, 105, 107, 111], "faq": 84, "far": [26, 49], "fast": [25, 47, 83, 85, 88, 89, 92, 96, 100, 109, 110], "faster": [88, 89, 94, 96, 110, 111], "fastsurf": [42, 46, 49, 58, 61, 62, 63, 66, 86, 90, 91, 93, 95, 99, 100, 102, 103, 104, 106, 108, 109, 110], "fastsurfer_": 89, "fastsurfer_colorlut": [103, 105], "fastsurfer_hom": [58, 86, 88, 90, 99, 109], "fastsurfer_reconsurf": 89, "fastsurfer_root": 107, "fastsurfercnn": [23, 81, 89, 92, 94, 101, 108, 110, 112], "fastsurfercnnbas": [42, 65], "fastsurferdir": [87, 105], "fastsurferroot": 94, "fastsurfervinn": [42, 83, 87, 88, 89, 96, 109, 110, 112], "fastsurfervinn_axi": 103, "fastsurfervinn_coron": 103, "fastsurfervinn_sagitt": 103, "featur": [24, 43, 85, 94, 96], "feder": [83, 96], "fee": 97, "feed": [34, 43], "feedforward": [41, 42, 43], "feel": 96, "fepegar": 14, "fetch": 85, "few": [89, 90, 92, 96], "fi": 100, "field": [13, 14, 33, 47, 58, 67, 72, 83, 88, 92, 95, 96, 100, 102, 107, 110], "fifth": 99, "fifti": 97, "fig": [31, 57], "figsiz": 31, "figur": [31, 57], "file": [13, 16, 18, 20, 31, 34, 35, 38, 39, 44, 46, 47, 49, 50, 51, 58, 61, 64, 66, 67, 70, 72, 73, 75, 78, 79, 85, 86, 87, 88, 89, 90, 92, 94, 95, 96, 97, 98, 99, 100, 102, 103, 104, 105, 106, 110, 111], "file_or_buff": 54, "file_save_nam": [31, 57], "fileexists_by_attribut": 50, "fileexists_in_subject_fold": 50, "filenam": [26, 39, 46, 49, 50, 58, 67, 70, 72, 73, 75, 78, 88, 91, 92, 99, 110], "filename1": 34, "filename2": 34, "filename_by_attribut": 50, "filename_in_subject_fold": 50, "filepath": [50, 51, 73, 79], "filesystem": 100, "fill": [21, 33, 47, 61, 75, 79, 86, 105], "fill_unknown_labels_per_hemi": 34, "filling_unknown_label": 21, "fillonlylabel": 79, "fillval": 47, "filter": [15, 20, 23, 34, 42, 47, 61, 79, 94, 106], "filter_blank_slic": 105, "filter_blank_slices_thick": [15, 20, 34], "filter_git_statu": 61, "filter_s": 47, "final": [63, 65, 66, 81, 86, 89, 94, 95, 103, 105, 109], "finalsurf": [86, 88, 110], "find": [16, 20, 21, 26, 31, 33, 34, 47, 49, 50, 54, 57, 67, 68, 70, 73, 78, 85, 87, 89, 90, 92, 100, 109, 110], "find_affin": 68, "find_all_island": 78, "find_devic": 50, "find_img_size_by_fov": 33, "find_latest_experi": 57, "find_min_s": 33, "find_rigid": 68, "find_rot": 68, "fine": [26, 49, 88, 91, 94, 110], "fine_tun": [26, 49], "finish": [46, 59, 87, 90, 94, 99, 100], "first": [14, 29, 33, 47, 54, 65, 67, 78, 79, 80, 83, 86, 88, 89, 92, 96, 98, 99, 100, 102, 103, 104, 109, 110, 111], "fischl": [83, 88, 90, 96, 109, 110], "fit": [47, 85, 87, 97], "five": 40, "fix": [73, 75, 76, 85, 86, 89], "flag": [34, 47, 50, 54, 58, 62, 75, 86, 89, 90, 95, 99, 100, 103, 109], "flag_nam": 50, "flex": 42, "flexibl": 90, "flip": [14, 15, 45, 62, 69], "flip_data": 45, "flip_wm_island": 45, "float": [15, 28, 29, 30, 33, 34, 39, 41, 44, 46, 47, 48, 50, 56, 59, 63, 64, 66, 67, 68, 69, 77, 78, 111], "float_gt_zero_and_le_on": 48, "floattensor": 41, "flow": 63, "fly": 89, "fn": [50, 56], "fname": 67, "focus": 84, "folder": [50, 87, 91, 94, 98, 99, 100], "follow": [28, 34, 50, 58, 66, 83, 84, 85, 86, 87, 88, 89, 90, 91, 94, 96, 97, 98, 100, 103, 106, 107, 109, 110, 111], "forc": [33, 47, 59, 85, 88, 103], "force_img_s": 33, "force_iso_vox": 33, "force_lia": 33, "force_lia_strict": 33, "forget": [87, 110], "fork": 85, "form": [30, 56, 97], "format": [33, 34, 35, 47, 61, 63, 67, 68, 72, 73, 90, 92, 98, 99, 100], "format_paramet": 47, "formatt": 47, "formula": 47, "fornix": 83, "forward": [23, 24, 41, 42, 43, 54, 65, 85], "foster": 84, "found": [49, 78, 86, 87, 100, 102, 103, 106, 110], "four": [40, 44, 99], "fp": 56, "fraction": [47, 111], "frame": 34, "free": [84, 87, 88, 96, 97, 98, 110], "freedom": 90, "freesurf": [21, 33, 34, 47, 68, 71, 83, 87, 88, 90, 91, 92, 94, 95, 98, 100, 102, 103, 105, 107, 110, 111], "freesurfer_hom": [86, 87, 88, 89, 90, 110], "freesurfercolorlut": [44, 47], "freeview": [86, 91, 92], "frequenc": [15, 31, 34, 38, 105], "from": [14, 15, 20, 21, 24, 26, 28, 31, 33, 34, 39, 43, 46, 47, 49, 50, 54, 57, 58, 61, 62, 64, 65, 66, 67, 68, 69, 70, 73, 78, 84, 85, 86, 87, 88, 89, 90, 91, 95, 96, 97, 98, 99, 100, 102, 103, 107, 110, 111], "from_seg": 111, "front_top_left": 40, "frozenset": 33, "fs60": 103, "fs_balabel": 81, "fs_licens": [86, 87, 88, 89, 90, 94, 98, 100, 110], "fs_version": 71, "fs_version_str": 71, "fsaparc": [88, 110], "fsavaerag": 70, "fsaverag": 90, "fslmer": 90, "fsqsphere": [88, 110], "fssl": 89, "fstess": [88, 110], "fstutori": 86, "fswiki": 86, "full": [15, 34, 38, 47, 50, 62, 71, 87, 89, 90, 92, 94, 95, 96, 98, 99, 102, 107, 109, 110, 112], "full_ipv": 47, "full_nbr_label": 47, "full_nbr_mean": 47, "full_pv": 47, "full_seg_mean": 47, "fulli": [23, 42, 83, 96, 99], "func": 50, "function": [14, 15, 18, 20, 23, 24, 25, 29, 30, 31, 33, 41, 42, 47, 50, 54, 56, 59, 61, 62, 65, 66, 70, 71, 74, 75, 81, 85, 89, 94, 99, 100, 105, 110], "fund": [83, 96], "further": [84, 91], "furthermor": [86, 87], "fuse": [23, 34, 42], "fuse_cortex_label": 34, "futur": [33, 34, 46, 47, 50, 59, 86, 88, 109], "future1": 34, "future2": 34, "fz": [104, 107], "g": [34, 47, 50, 54, 61, 69, 70, 73, 75, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 96, 99, 100, 102, 103, 104, 105, 107, 110, 111], "gamma": 68, "gap": 21, "gaussian": [14, 32, 43], "gaussiannois": 43, "gb": [89, 94, 96, 100], "gckeepstorag": 94, "gcpolici": 94, "geforc": 92, "gen": 85, "gender": 84, "gener": [14, 28, 34, 54, 61, 66, 87, 88, 90, 91, 92, 95, 97, 99, 100, 107, 110], "generate_bias_field": 14, "generate_binary_structur": 30, "generate_hdf5": [81, 108, 112], "geometri": 91, "german": [83, 96], "get": [15, 23, 24, 28, 32, 33, 34, 35, 42, 43, 46, 47, 49, 50, 60, 61, 63, 64, 67, 87, 88, 89, 92, 94, 96], "get_adjm": 79, "get_aseg_cereb_mask": 15, "get_attribut": 50, "get_bounding_offset": 16, "get_brain_centroid": 67, "get_cfg": [39, 64], "get_checkpoint": [26, 49], "get_checkpoint_path": [26, 49], "get_color_by_index": 54, "get_common_suffix": 50, "get_config": [27, 51], "get_conformed_vox_img_s": 33, "get_dataload": [17, 36], "get_default_version_info": 61, "get_devic": [39, 64], "get_epoch_lr": 28, "get_image_mean": 67, "get_img": 46, "get_img_metadata": 16, "get_label": 16, "get_labels_from_lut": 34, "get_largest_cc": 34, "get_loss_func": 41, "get_lr": 28, "get_lr_schedul": [28, 53], "get_max_s": [39, 64], "get_model_height": [39, 64], "get_model_width": [39, 64], "get_modelnam": [39, 64], "get_nibabel_img": 16, "get_num_class": [39, 46, 64], "get_num_thread": 60, "get_orig": 16, "get_plan": [39, 64], "get_predict": [46, 66], "get_random_param": 14, "get_region_bg_intersection_mask": 44, "get_seg_centroid": 69, "get_subject_nam": [16, 35, 46], "get_tal_origin_voxel": 67, "get_thick_slic": 34, "get_ventricle_bg_intersection_volum": 44, "get_vox2ra": 69, "getitem_by_index": 54, "getscal": 33, "getsurfcorrespond": 73, "getter": 46, "gihub": 85, "gil": 34, "gist_ncar": 54, "git": [61, 71, 85, 87, 88, 89, 94], "git_branch": [61, 88], "git_hash": 61, "git_process": 61, "git_statu": 61, "github": [14, 85, 87, 89, 90, 93, 94], "githubusercont": 89, "give": [41, 46, 50, 53, 88, 97, 110], "given": [13, 18, 20, 25, 26, 27, 28, 30, 32, 34, 36, 38, 41, 44, 46, 48, 49, 50, 51, 63, 64, 70, 78, 87, 96, 98, 99, 103, 106, 110], "glibcxx": 89, "glob": 100, "global": [23, 29, 42, 47, 87, 88, 90, 94, 98], "global_crop": 47, "global_stat": 47, "global_step": [29, 55], "gm": [78, 83, 90, 105], "gm_binari": 21, "gm_mask": 38, "gn": 43, "gn0": 43, "gn1": 43, "gn2": 43, "gn3": 43, "gn4": 43, "gn_nois": 35, "go": [47, 85, 94], "goal": 90, "good": 84, "goodwil": 97, "googl": 95, "gpu": [26, 49, 83, 87, 88, 90, 92, 96, 99, 100, 102, 103, 106, 107, 111], "gpu_partit": 87, "gracefulli": 84, "gradient": [34, 38, 105], "grai": [21, 34, 86, 91], "grant": 97, "graph": [23, 24, 42, 43], "graphic": [89, 96], "great": 96, "greater": [48, 87, 88, 89], "grei": 34, "grep": 100, "greve": 90, "grid": 30, "grossli": 97, "ground": [29, 34, 38, 56, 105], "group": [14, 30, 47, 56, 87, 89, 90, 94, 96, 100], "grow": 47, "gt": [29, 30, 34], "gt_name": 105, "gt_nocc": 105, "guarante": [67, 111], "guess": 34, "gui": 85, "guid": [47, 85, 87, 89, 98], "guidelin": 85, "gyri": 86, "gz": [66, 87, 88, 91, 92, 94, 99, 100, 102, 103, 107], "h": [15, 41, 42, 43, 47, 85, 87, 88, 102, 103, 104, 105, 106, 107, 109, 110], "h5py": [38, 89], "h5pydataset": 38, "ha": [41, 50, 65, 67, 70, 85, 87, 88, 89, 90, 94, 96, 97, 98, 99, 105, 107], "had": 89, "half": [87, 88], "handi": 92, "handl": [46, 47, 50, 54, 65], "handle_cuda_memory_except": 50, "happen": [85, 100], "harass": 84, "hard": [34, 85, 86], "hardwar": [94, 102, 103, 107, 111], "harm": [84, 86], "harmless": 97, "harvard": [86, 87, 88, 92, 98, 110], "has_attribut": 50, "has_git": 61, "hash": [61, 71, 94], "hausdorff": 30, "have": [14, 20, 30, 34, 50, 56, 65, 66, 68, 78, 84, 85, 86, 87, 88, 89, 90, 91, 92, 94, 96, 97, 99, 100, 102, 103, 105, 107, 110], "hd": [30, 88, 109], "hd50": 30, "hd95": 30, "hdf5": [18, 38, 89, 105, 106], "hdf5_dir": 89, "hdf5_name": 105, "hdf5_set": [105, 106], "head": [88, 89, 90, 92, 96, 102, 103, 107, 109, 110], "header": [13, 21, 33, 34, 47, 54, 66, 72, 73, 75, 111], "header_info": 34, "heavi": 87, "height": [13, 39, 42, 64, 65, 106], "help": [46, 47, 50, 58, 85, 86, 87, 88, 89, 90, 94, 96, 99, 100, 108, 110], "helper": [87, 90], "helpformatt": 47, "hemi": [34, 70, 95, 110], "hemispher": [34, 38, 45, 70, 87, 88, 91, 99, 110], "henschel": [83, 88, 96, 109, 110], "here": [70, 84, 87, 88, 89, 90, 92, 94, 96, 98, 100, 103, 105, 109], "herebi": 97, "herein": 97, "hhmmss": 100, "hidden": 99, "high": [33, 34, 83, 88, 96, 107, 109], "higher": [33, 78, 89], "highest": 33, "highli": [83, 90], "highlight": 90, "highr": [83, 88, 96, 109, 110, 111], "hint": 54, "hippocampu": 96, "hire": [34, 38, 105, 110], "hires_w": 105, "hires_weight": 38, "histori": 85, "hold": [33, 44, 45, 51, 67, 69, 70, 71, 73, 74, 75, 76, 77, 78, 79, 80, 97], "hole": [21, 79], "home": [49, 86, 87, 88, 89, 90, 92, 94, 99, 100, 102, 103, 106, 107, 109, 110], "homebrew": 89, "homer": 98, "homogen": 68, "hook": 39, "hope": 86, "horizont": 14, "host": [49, 89, 94, 98], "hot": [56, 88], "hous": 96, "how": [33, 47, 86, 87, 89, 92, 93, 94, 95, 96, 98], "howev": [33, 86, 87, 97, 100, 107, 110, 111], "hpc": [94, 98], "hpcwork": [87, 100], "hsa_override_gfx_vers": 94, "html": [28, 84, 87, 88, 89, 94, 98, 110], "http": [14, 25, 28, 83, 84, 85, 86, 87, 88, 89, 90, 92, 94, 96, 97, 98, 104, 107, 109, 110, 111], "httperror": 49, "hub": 94, "human": [89, 96], "hyperintens": 14, "hypo_map_label2subseg": 62, "hypo_map_prediction_sagittal2ful": 62, "hypo_map_subseg_2_fsseg": 62, "hypo_maskfil": 66, "hypo_segfil": [66, 107], "hypointens": 34, "hypoth": 83, "hypothalam": [83, 92, 96, 107], "hypothalamu": [66, 83, 86, 88, 91, 96, 107, 109], "hypothalamus_mask": [66, 91, 107], "hypterthread": 87, "hypvinn": [81, 83, 88, 95, 96, 99, 101, 104, 108, 109], "hypvinn_axial_v1": 107, "hypvinn_coronal_v1": 107, "hypvinn_qc_screenshoot": 107, "hypvinn_sagittal_v1": 107, "hypvinn_seg": 107, "hypvinndataset": 63, "i": [14, 15, 20, 21, 25, 26, 28, 29, 30, 33, 34, 41, 44, 46, 47, 48, 49, 50, 53, 54, 56, 58, 59, 61, 62, 64, 65, 66, 67, 69, 70, 73, 75, 76, 78, 79, 80, 81, 83, 84, 86, 87, 88, 89, 91, 92, 94, 95, 96, 97, 98, 99, 100, 102, 103, 104, 105, 106, 107, 109, 110, 111], "i1": 90, "icon": 92, "icv": [87, 88], "id": [15, 19, 33, 34, 38, 44, 47, 50, 54, 66, 69, 70, 71, 73, 77, 78, 79, 87, 88, 89, 90, 92, 94, 98, 100, 102, 103, 105, 107, 109, 110, 111], "idea": [85, 90], "ideal": 99, "ident": [68, 79, 84, 85, 88, 94], "identif": 94, "identifi": [15, 85, 100], "idx": 31, "ignor": [33, 41, 61, 88, 107, 111], "ignore_fs_vers": [88, 110], "ignore_index": 41, "ii": [88, 89, 97, 99, 109], "iii": [89, 97, 99], "imag": [13, 14, 15, 18, 20, 21, 23, 24, 29, 30, 32, 33, 34, 35, 38, 39, 40, 42, 43, 46, 47, 50, 54, 57, 62, 63, 65, 66, 67, 69, 78, 83, 86, 87, 88, 89, 90, 91, 92, 95, 96, 99, 100, 102, 103, 105, 106, 109, 110, 111], "imag_a_00034": [83, 88, 96, 107, 109], "image2": 34, "image_nam": [46, 105], "image_path": 100, "image_shap": 20, "imageri": 84, "images_batch": [31, 57], "img": [15, 20, 31, 32, 33, 34, 35, 38, 62, 69, 78], "img1": 47, "img2": 47, "img_arrai": 34, "img_batch": 29, "img_data": [13, 21, 34, 62], "img_filenam": [34, 39], "img_kei": 15, "img_label": 78, "img_lut": 78, "img_org": 16, "img_path": 13, "img_siz": [33, 47], "img_vol": 34, "imglut": 78, "impact": [88, 102, 103, 107, 111], "implement": [14, 25, 41, 47, 54, 89, 94, 100], "impli": [30, 88, 97], "implicitli": [20, 61], "import": [34, 58, 86, 88, 91, 97, 111], "imposs": 86, "improperli": 76, "improv": [86, 96, 97], "in_cooldown": 28, "in_dir": [58, 102, 103], "inabl": 97, "inaccur": 86, "inaccuraci": [33, 86], "inaparcnam": 79, "inappropri": 84, "incid": 84, "incident": 97, "incl": 91, "includ": [13, 14, 15, 22, 33, 34, 47, 50, 54, 61, 65, 71, 79, 83, 84, 85, 86, 87, 88, 89, 91, 92, 93, 94, 97, 98, 103, 105, 106, 107, 110], "inclus": [84, 97], "incompat": [85, 94, 98, 102], "inconsist": [20, 34, 66], "incorpor": 97, "incortexnam": 79, "increas": [33, 90, 94, 96, 100], "incur": 97, "indemn": 97, "indemnifi": 97, "indent_incr": 47, "independ": [83, 88, 90, 94, 96, 99, 107, 109, 110], "index": [20, 34, 41, 47, 54, 63, 73], "indic": [24, 25, 43, 47, 78, 86, 90, 97, 100], "indirect": 97, "indirectli": 111, "individu": [84, 85, 88, 90, 96, 97, 99, 100, 110], "induc": 90, "infer": [25, 35, 46, 47, 63, 66, 81, 88, 102, 103, 107, 111], "infer_labels_excludeid": 47, "infer_mapping_from_lut": 34, "infer_merged_label": 47, "infin": 48, "inflat": [88, 91, 110], "influenc": 30, "info": [20, 33, 61, 72, 88, 94], "inform": [13, 20, 33, 34, 47, 48, 61, 63, 70, 75, 83, 84, 85, 86, 88, 89, 90, 92, 94, 97, 98, 103, 107, 110], "infring": 97, "inher": 90, "inherit": 86, "init_pr": 39, "initi": [27, 30, 39, 42, 47, 51, 56, 62, 65, 83, 86, 88, 90, 91, 96], "inner": [34, 78], "inp_block": 42, "inplac": [39, 47], "input": [14, 23, 24, 29, 30, 32, 33, 34, 38, 41, 42, 43, 45, 47, 50, 54, 56, 61, 62, 63, 65, 66, 67, 75, 76, 79, 83, 85, 86, 87, 88, 90, 99, 102, 103, 105, 106, 109, 110, 111], "input_dir": 70, "input_norm": 111, "input_seg": 111, "inputdenseblock": [43, 65], "inputx": 41, "insid": [46, 67, 78, 79, 87, 88, 94, 98, 109], "inspect": [86, 87], "inspir": 25, "instal": [61, 87, 88, 90, 92, 94, 95, 96, 98, 99, 104], "install_env": 89, "instanc": [64, 65, 84], "instead": [23, 33, 42, 47, 58, 75, 80, 85, 86, 88, 92, 98, 105, 110], "institut": 97, "instruct": [87, 89, 92], "insult": 84, "insurf": 75, "insurfnam": 79, "int": [13, 15, 16, 20, 25, 26, 28, 29, 30, 33, 34, 38, 39, 41, 44, 45, 46, 47, 48, 49, 50, 54, 55, 56, 57, 60, 61, 62, 63, 64, 65, 66, 67, 69, 71, 78, 79, 80, 88, 110], "int8": 47, "int_ge_zero": 48, "int_gt_zero": 48, "integ": [41, 44, 47, 48, 54, 79, 111], "integr": 86, "intend": [33, 86, 95, 98], "intens": [14, 33, 47, 67, 111], "intention": 97, "interact": 92, "interest": [34, 47, 84, 92], "interfac": [71, 73, 74, 75, 76, 77, 78, 79, 80, 85, 97, 102, 107, 110, 112], "interleav": [99, 110], "intermedi": [86, 87, 88, 100, 102, 103, 110], "intern": [30, 50, 54, 62, 81, 90, 105], "interpol": [20, 33, 34, 40, 42, 43, 65, 106], "interpol1": [42, 65], "interpol2": [42, 65], "interpolation_lay": 81, "interpolation_mod": [40, 42, 65], "interpret": [50, 85, 111], "intersect": [30, 44, 56], "intersection_volum": 44, "intervent": 86, "intracrani": [86, 92], "intricaci": 87, "introduct": [90, 92, 95], "introduction_to_amd_rocm_installation_guide_for_linux": 89, "invalid": [20, 47, 48, 65, 66, 67, 100], "invers": [33, 54, 90], "investig": 84, "invit": 86, "invok": [87, 110], "io": [87, 89, 94, 100], "ioerror": 34, "iornt": 62, "iou_scor": 56, "ipc": 89, "ipv": 47, "irrevoc": 97, "is_bett": 28, "is_biject": 54, "is_checkpoint_epoch": 26, "is_conform": 33, "is_int": 54, "is_lia": 33, "is_resampling_vox2vox": 33, "island": [45, 78], "isol": 85, "isometr": 88, "isotrop": [33, 34, 78, 83, 87, 88, 103, 110], "issu": [84, 85, 86, 89, 90, 93, 97], "item": [47, 50], "iter": [29, 34, 45, 47, 50, 55, 58, 64, 67, 86, 88, 110], "itk": [67, 88, 110], "itk_aseg": 67, "itk_bfcorr_imag": 67, "itk_imag": 67, "itk_mask": 67, "itk_n4_bfcorrect": 67, "its": [13, 14, 46, 54, 59, 67, 79, 84, 87, 89, 94, 97, 98, 102, 103, 110], "itself": [103, 107], "j": [25, 78, 83, 88, 90, 96, 109, 110], "januari": 97, "job": [87, 100], "job_arrai": 100, "jobarrai": [99, 100], "jobarrayid": 100, "joint": 90, "json": [54, 94], "jsoncolorlookupt": 54, "juelich": [104, 107], "just": [20, 33, 70, 76, 85, 87, 88, 89, 90, 92, 98, 110], "j\u00fclich": 107, "k": [14, 83, 88, 92, 96, 109, 110], "kdtree": 73, "keep": [14, 33, 34, 54, 55, 85, 111], "keep_label": 54, "keep_strictly_posit": 14, "keepbyt": 94, "keepdur": 94, "kei": [15, 47, 54, 58, 61, 66, 88, 94, 110], "kernel": [47, 89, 94, 106], "kernel_c": [24, 43], "kernel_h": [24, 43, 106], "kernel_w": [24, 43, 106], "keypair": 94, "keyword": [34, 47, 50, 80], "kfd": [89, 94], "kill": 100, "kind": 97, "know": 90, "kpend": 100, "kt": 54, "kuegler": [25, 54, 83, 88, 96, 99, 100, 109, 110], "kueglrun": 100, "kuegpend": 100, "kuegrun": 100, "kwarg": [28, 34, 47, 50, 58, 59, 80], "k\u00fcgler": [99, 100, 107, 111], "l": [83, 85, 88, 96, 109, 110], "lab": 47, "label": [13, 14, 15, 20, 21, 29, 30, 31, 32, 34, 35, 38, 41, 44, 45, 47, 54, 55, 57, 62, 67, 69, 70, 73, 77, 78, 79, 83, 85, 86, 91, 96, 103, 105, 110, 111], "label_batch": 29, "label_extract": 34, "label_id": [69, 77], "label_list": 14, "label_map": 15, "label_nam": 70, "label_typ": [15, 20], "label_vol": 34, "labeldir": 70, "labelnam": [34, 47, 73, 105], "labelname2id": 54, "labelname2index": 54, "labels_batch": [31, 57], "labels_dst": 77, "labels_list": 14, "labels_mov": 77, "labels_new": 79, "labels_sag": [34, 38], "lambda": [30, 56], "landau": 94, "languag": 84, "laplac": 47, "larg": [47, 83, 91, 94, 96, 103, 111], "larger": [70, 87, 89], "largest": [16, 34, 78, 89, 103, 111], "last": [20, 24, 26, 31, 43, 61, 92, 102, 103, 107, 111], "last_epoch": 28, "later": [34, 38, 44, 86, 89, 92, 109], "latest": [57, 85, 87, 89, 92, 94, 98, 110], "latter": [94, 100], "law": 97, "lawsuit": 97, "layer": [23, 24, 34, 42, 43, 63, 65, 106], "layout": 33, "lbl_data": 15, "lbl_kei": 15, "lbl_path": 13, "lbl_type": 15, "lead": [20, 48, 58, 90], "leadership": 84, "learn": [14, 25, 28, 29, 53, 55, 63, 74, 83, 88, 96, 99, 102, 106, 109, 110], "learnabl": 43, "least": [68, 88, 89, 96, 97], "leav": 61, "left": [15, 21, 34, 38, 44, 47, 53, 69, 87, 91, 99, 103, 105], "legaci": 47, "legacy_freesurf": [47, 111], "legal": 97, "len": 14, "length": [14, 30], "less": [20, 92, 96], "let": 96, "level": [48, 66, 67, 84, 94], "lh": [34, 70, 73, 86, 91], "lhcerebralwhitematt": 111, "lhcortex": 111, "lhsurfacehol": 111, "lia": [15, 33, 87, 110], "liabil": 97, "liabl": [96, 97], "lib": 94, "librari": [85, 103, 106], "libstdc": 89, "licens": [86, 87, 88, 89, 90, 92, 94, 95, 96, 98, 99, 100, 110], "licensor": 97, "like": [34, 47, 58, 61, 67, 71, 89, 94, 99, 100, 103], "likelihood": 41, "limit": [47, 94, 97, 99, 100, 103], "line": [25, 33, 44, 45, 47, 61, 66, 67, 69, 70, 71, 73, 74, 75, 76, 77, 78, 79, 80, 85, 87, 89, 99, 100, 103, 106, 110], "linear": [28, 33, 34, 72, 90], "linearsegmentedcolormap": [31, 57], "link": [54, 87, 91, 92, 96, 97], "linux": [85, 92, 94, 95], "list": [14, 26, 29, 31, 34, 35, 38, 46, 47, 49, 50, 54, 57, 58, 61, 69, 70, 71, 73, 78, 79, 84, 86, 89, 94, 95, 97, 98, 100, 103, 105, 106, 108, 109, 110, 111], "liter": [16, 47, 58], "litig": 97, "littl": 88, "lme": 90, "load": [13, 16, 17, 18, 19, 22, 26, 27, 31, 33, 34, 35, 36, 38, 39, 49, 51, 57, 58, 63, 64, 66, 73, 94, 99, 102, 103, 104, 105, 106], "load_and_conform_imag": 34, "load_aux_data": [16, 18, 19], "load_checkpoint": [39, 64], "load_checkpoint_config": 49, "load_checkpoint_config_default": 49, "load_classwise_weight": 31, "load_config": 81, "load_data": 81, "load_from_checkpoint": [26, 49], "load_imag": 34, "load_maybe_conform": 34, "load_subject": 19, "load_test_subject": 19, "load_volum": 66, "loaded_epoch": [26, 49], "loader": [16, 19, 39, 57, 81], "loc": 75, "local": [34, 47, 85, 87, 88, 92, 94, 98, 110], "local_rank": [30, 56], "locat": [47, 61, 87, 88, 90, 94, 102, 103, 109, 110], "locate_mask_bbox": 16, "locating_unknown": 21, "log": [29, 33, 34, 41, 55, 80, 81, 85, 88, 91, 100, 102, 103, 106, 107, 110], "log_dir": [26, 49, 106], "log_epoch": [29, 55], "log_file_path": 52, "log_it": [29, 55], "log_lr": 29, "log_nam": [102, 103, 107], "logfil": [52, 91, 99, 103], "logger": [33, 34], "logit": [23, 24, 42, 43, 65], "long": [41, 88, 90, 108, 110], "long_fastsurf": [88, 90, 108], "long_prepare_templ": [88, 90], "longer": [89, 92, 94], "longitudin": [14, 88, 95, 109, 110], "longitudion": 90, "longtensor": 41, "look": [20, 34, 62, 78, 85, 92, 99, 100], "lookup": [34, 47, 103, 105], "loop": 99, "loss": [23, 29, 42, 55, 81, 97], "loss_c": 55, "loss_dic": 55, "loss_dict": 29, "loss_tot": 55, "lot": 85, "low": 33, "lower": [24, 43], "lr": [28, 29, 53, 55], "lr_func_cosin": 28, "lr_restart": 28, "lr_schedul": [81, 106], "lta": [20, 81, 86, 107], "ltadict": 20, "lut": [34, 38, 39, 46, 47, 92, 103, 105, 111], "lut_fil": 34, "m": [78, 79, 83, 87, 88, 89, 96, 99, 107, 109, 110], "m1": [89, 94], "m1_inp_block": 65, "m2": 89, "m2_inp_block": 65, "mac": [88, 89, 94], "machin": [92, 94, 100], "maco": [85, 95], "made": [97, 100], "mai": [20, 61, 84, 86, 87, 88, 89, 91, 94, 96, 97, 99, 100, 102, 103, 107, 110], "mail": [84, 97], "main": [13, 25, 42, 47, 50, 61, 66, 70, 79, 83, 89, 94, 103, 106, 110], "main_segfil": [50, 88], "maintain": [84, 85], "major": 85, "make": [69, 75, 84, 85, 87, 89, 90, 94, 96, 97, 98, 110], "make_argu": 47, "make_classmapp": 54, "make_pars": [33, 46, 61, 76], "make_subjects_dir": 50, "malfunct": 97, "mame": 54, "mammilar": 83, "man": 86, "manag": [22, 47, 85, 87, 89, 97], "mandatori": 88, "manedit": [86, 88, 110], "mani": [47, 85, 87, 88, 91, 94], "manifold": 78, "manner": 99, "manual": [87, 88, 94, 95, 98, 99], "manual_cereb": 21, "map": [15, 20, 23, 24, 29, 31, 33, 34, 38, 39, 43, 47, 50, 54, 57, 58, 62, 70, 73, 74, 77, 83, 86, 87, 88, 90, 91, 92, 94, 96, 98, 105, 110], "map_aparc_aseg2label": 34, "map_imag": 33, "map_label2aparc_aseg": 34, "map_label2subseg": 20, "map_logit": 54, "map_multiple_label": 70, "map_prediction_sagittal2ful": [15, 34], "map_prob": 54, "map_sag2label": 15, "map_siz": 20, "map_surf_label": 81, "mapped_aseg": 34, "mapped_subseg": [20, 62], "mapper": 81, "mapsurflabel": 73, "march": [75, 88], "mark": [85, 97], "martin": [84, 107], "mask": [15, 16, 21, 32, 34, 38, 44, 45, 47, 58, 66, 67, 70, 79, 86, 87, 91, 92, 103, 105, 107, 110, 111], "mask_fil": 110, "mask_nam": [88, 110], "maskvol": 111, "mass": 90, "massiv": 94, "match": [33, 34, 38, 63, 103, 105], "materi": 94, "matlab": 90, "matplotlib": [31, 57], "matric": [56, 88], "matrix": [13, 29, 31, 33, 55, 56, 57, 67, 68, 69, 77, 78, 79, 86], "matter": [14, 21, 34, 45, 61, 67, 70, 91, 95], "max": [24, 33, 38, 39, 43, 47, 54, 87, 88, 99, 105, 109, 110], "max0": 16, "max1": 16, "max_edge_weight": [15, 34], "max_epoch": 28, "max_help_posit": 47, "max_hires_weight": 34, "max_it": 28, "max_label": [47, 54], "max_siz": 33, "max_unpool2d": 89, "max_w": 105, "max_weight": [34, 38], "maxim": [33, 34], "maximum": [15, 30, 39, 47, 50, 54, 64, 67, 111], "maximum_intens": 47, "maxout": [23, 24, 42, 43], "maxpool": [24, 43], "mayb": [46, 85], "md5sum": 61, "mean": [14, 29, 30, 32, 41, 47, 56, 62, 67, 87, 88, 97, 103, 110, 111], "mean_filt": 34, "meantim": 85, "measur": [47, 96], "measure_onli": 111, "measurefil": [47, 111], "mechan": 97, "media": [84, 97], "median": [14, 15, 31, 34, 38, 105], "medium": 97, "meet": 97, "mem": 100, "mem_seg": 100, "mem_surf": 100, "member": [84, 85], "memori": [20, 50, 88, 89, 94, 96, 99, 100, 102, 103, 107], "mention": 111, "merchant": 97, "mere": 97, "merg": [47, 54, 85, 88, 96], "merge_label": 47, "merge_labels_start": 47, "merged_label": [47, 111], "merit": 85, "mesh": 79, "messag": [25, 33, 34, 39, 47, 50, 54, 59, 61, 66, 102, 103, 107], "messagebuff": 59, "met": 94, "meta": 47, "meter": 81, "method": [14, 16, 18, 19, 20, 22, 23, 24, 25, 28, 29, 30, 32, 35, 38, 39, 40, 41, 42, 43, 46, 47, 49, 50, 54, 55, 56, 58, 59, 61, 63, 64, 65, 83, 85, 88, 96, 106, 107, 109, 110], "methodolog": 90, "metric": [26, 28, 29, 49, 81, 103, 111], "metrics_per_class": 29, "mgh": [21, 86, 87, 88, 92, 98, 110], "mghimag": [33, 34], "mgz": [34, 58, 69, 75, 86, 87, 88, 89, 90, 91, 92, 96, 98, 100, 102, 103, 105, 107, 110, 111], "mi": [84, 85, 87, 89, 90], "mid": [69, 90], "mid_slic": 69, "middl": [23, 34, 42], "might": [92, 94, 98, 99], "millimet": 83, "mimic": 83, "min": [33, 34, 46, 47, 48, 88, 96, 103, 110], "min0": 16, "min1": 16, "min_dim": 33, "min_memori": 50, "mind": 85, "miniconda": 89, "miniconda3": 89, "minim": [33, 34, 58, 88], "minimum": [33, 34, 47, 50, 89, 103], "minimum_intens": 47, "ministri": [83, 96], "minor": [85, 86], "minut": [83, 87, 92, 96, 100], "misc": [81, 112], "miss": [21, 47, 56, 61, 66, 70, 72, 86, 89, 100], "mix": [90, 111], "mixing_coeff": [47, 111], "mkdir": 92, "mm": [30, 33, 78, 92], "mmb": [83, 88, 96, 109], "mod_weight": 65, "modal": [63, 64, 65, 66, 107], "modalitydict": [64, 66], "modalitymod": [64, 66], "mode": [17, 29, 33, 36, 42, 47, 55, 63, 64, 65, 66, 79, 88, 89, 94, 99, 110], "mode_filt": 79, "model": [22, 26, 30, 39, 46, 49, 56, 63, 64, 66, 81, 90, 91, 92, 104, 112], "model_nam": [39, 64, 106], "model_parallel": 39, "modern": 89, "modif": [97, 100], "modifi": [34, 74, 86, 90, 97, 111], "modul": [26, 39, 49, 64, 66, 80, 81, 86, 89, 92, 95, 103, 106, 107], "moment": 94, "momentum": 106, "monei": 90, "moniqu": 107, "more": [30, 33, 48, 50, 68, 86, 87, 88, 90, 92, 94, 97, 98, 99, 107, 111], "morphologi": 30, "most": [30, 34, 47, 56, 85, 86, 87, 88, 89, 90, 94, 96, 100, 102, 107, 110], "motion": 96, "mount": [87, 88, 94, 99, 110], "mousa": [83, 88, 96, 107, 109], "mov": 69, "move": [15, 39, 62, 73, 77, 87, 100], "mp": [88, 89, 94], "mr": [47, 88, 96, 110, 111], "mri": [13, 14, 34, 35, 58, 63, 83, 86, 87, 88, 89, 90, 91, 92, 94, 96, 98, 100, 102, 103, 105, 107, 109, 110, 111], "mri_convert": 33, "mri_coreg": [88, 107], "mri_mc": [88, 110], "mri_robust_regist": [88, 107], "mri_robust_templ": 90, "mri_segstat": [47, 111], "mri_tessel": [88, 110], "mri_vol2vol": 107, "mri_volum": 103, "mris_preproc": 90, "mris_regist": 68, "much": [47, 85, 89, 94, 96], "mul": 47, "multi": [30, 47, 56, 88, 102, 103, 106, 107, 111], "multipl": [34, 47, 70, 71, 89, 90, 94, 95, 99, 103], "multires_coron": 105, "multiscaledataset": 35, "multiscaledatasetv": 35, "multiscaleorigdatathickslic": 35, "must": [14, 20, 30, 33, 47, 48, 88, 94, 97, 98, 100, 103, 110], "must_keep_id": 47, "mutablesequ": [26, 49], "my": [85, 92], "my_fastsurf": [89, 94], "my_fastsurfeer_analysi": 110, "my_fastsurfer_analysi": [86, 87, 89, 90, 94, 98, 110], "my_fs_license_dir": [87, 89, 90, 94, 98, 110], "my_mri_data": [87, 89, 90, 94, 98, 110], "my_recon_surf_output": 110, "my_segmentation_data": 110, "my_singlarity_imag": 98, "myaccount": 94, "myimag": 98, "n": [20, 34, 41, 42, 43, 62, 67, 78, 79, 87, 99, 100, 107, 109], "n4_bias_correct": 81, "n_epoch": 28, "n_iter": 28, "na": [83, 88, 96, 109], "name": [13, 15, 26, 31, 34, 35, 38, 39, 47, 49, 50, 54, 57, 58, 61, 64, 66, 70, 71, 73, 75, 76, 78, 79, 86, 87, 88, 90, 94, 96, 97, 98, 100, 110], "name1": 47, "name2": 47, "namespac": [25, 47, 51, 67, 71, 73, 74, 75, 76, 77, 78, 79, 80], "nation": 84, "nativ": [54, 83, 86, 88, 94, 95, 96, 99, 104], "native_t1_fil": 50, "nbr": 47, "nbr_mean": 47, "nbr_mixing_coeff": 47, "nclass": 56, "ndarrai": [13, 14, 15, 20, 31, 32, 33, 34, 35, 38, 39, 44, 45, 46, 47, 54, 56, 57, 62, 63, 64, 66, 67, 68, 69, 70, 73, 77, 78, 79], "ndimag": 30, "nearest": [33, 34, 40, 65], "necessari": [47, 84, 85, 86, 87, 89, 98, 100], "necessarili": 97, "need": [15, 20, 26, 33, 34, 70, 78, 83, 85, 86, 87, 88, 89, 90, 91, 92, 94, 98, 100, 102, 103, 106, 107, 109, 110], "neg": [20, 41, 48, 56, 79], "neglig": 97, "neighbor": 47, "neighborhood": 47, "neighbourhood": 30, "neither": [20, 48], "nesterov": 106, "net": 94, "network": [15, 16, 26, 28, 34, 35, 39, 46, 49, 56, 62, 63, 81, 83, 86, 88, 89, 103, 104, 106, 110], "neural": [39, 86, 88, 89, 104], "neuroimag": [22, 25, 83, 88, 90, 96, 109, 110], "neurosci": [83, 88, 96, 107, 109], "never": [33, 47, 85], "new": [33, 54, 62, 79, 85, 86, 89, 90, 94], "new_iornt": 62, "newer": 89, "newest": 94, "newlin": 47, "next": [50, 85, 88, 89, 90], "next_messag": 59, "ni": 85, "nib": [33, 34, 46, 92], "nibabel": [13, 34, 47, 62, 78, 79, 111], "niclei": 90, "nifti": [13, 33, 34, 90, 92], "nifti1head": 13, "nifti1imag": [33, 62], "nifti2head": 13, "nifti2imag": 33, "niftynet": 14, "nii": [66, 87, 88, 91, 92, 94, 99, 100, 102, 103, 107], "nipi": 111, "nj": [88, 109], "nll_loss": 41, "nmr": [86, 87, 88, 92, 98, 110], "nn": [26, 39, 49, 64, 65], "no_asegdkt": [83, 88], "no_bias_field": 83, "no_biasfield": [83, 87, 88, 92], "no_cereb": [83, 86, 87, 88, 91, 92, 100], "no_fs_t1": [88, 110], "no_grad": 105, "no_hypoth": [83, 86, 87, 88, 91, 92], "no_surfreg": [88, 110], "node": [26, 31, 36, 39, 41, 42, 46, 49, 51, 53, 64, 65, 66, 87, 100], "nois": [32, 43], "nomenclatur": 91, "non": [20, 29, 47, 59, 78, 79, 88, 89, 97], "none": [14, 16, 19, 20, 26, 28, 29, 30, 31, 33, 34, 35, 39, 41, 42, 46, 47, 48, 49, 50, 53, 54, 55, 56, 58, 59, 61, 63, 64, 65, 66, 67, 69, 70, 73, 76, 77, 78, 79, 88, 102, 105, 106, 107, 111], "nor": 20, "norm": [24, 43, 47, 67, 88, 102, 110, 111], "norm_nam": [47, 88, 102, 111], "norm_unit": [47, 111], "normal": [23, 42, 43, 47, 65, 67, 78, 88, 97, 105, 110], "normalize_img": 67, "normalize_weight": 65, "normalize_wm_aseg": 67, "normalize_wm_mask_bal": 67, "normalized_imag": 67, "normfil": [47, 111], "normmax": 47, "normmin": 47, "not_empti": 47, "note": [20, 28, 30, 33, 44, 58, 61, 74, 83, 86, 87, 88, 89, 90, 91, 94, 98, 99, 100, 102, 103, 107, 110, 111], "noth": 97, "notic": [86, 94, 97], "notimplementederror": 41, "notwithstand": 97, "nov": [99, 100], "novel": 88, "novot": 79, "now": [89, 94, 96], "np": [15, 20, 29, 31, 32, 33, 34, 35, 38, 44, 45, 46, 47, 56, 62, 63, 67, 73, 78, 79], "npt": [34, 35, 38, 39, 45, 47, 57, 62, 63, 64, 66, 67, 68, 69, 70, 72, 73, 74, 77, 79], "nt": 47, "nu": [88, 110], "null": 100, "num_cases_per_task": 100, "num_channel": [24, 43, 65, 106], "num_class": [24, 30, 34, 43, 56, 65, 106], "num_classes_ful": 34, "num_cpus_per_case_surf": 100, "num_cpus_per_task": 100, "num_epoch": 106, "num_filt": [24, 43, 106], "num_gpu": [26, 49, 106], "num_seg_process": 99, "num_seg_thread": 99, "num_surf_process": 99, "num_surf_thread": 99, "number": [14, 15, 20, 23, 26, 28, 29, 30, 31, 32, 33, 34, 38, 39, 42, 45, 46, 47, 48, 49, 50, 56, 57, 60, 61, 63, 64, 66, 67, 70, 71, 73, 78, 79, 87, 88, 89, 90, 91, 98, 99, 100, 102, 103, 105, 106, 107, 109, 110, 111], "number_of_voxel": 47, "number_of_within_robustness_threshold": 47, "numer": 47, "numit": 67, "numpi": [14, 20, 34, 44, 45, 47, 48, 54, 73, 111], "nv": [87, 90, 92, 98, 99], "nvidia": [88, 89, 94, 96, 102, 103, 107, 111], "nvoxel": 47, "nx3": 73, "o": [26, 39, 49, 66, 70, 85, 89, 92, 94, 110, 111], "ob": 38, "object": [28, 30, 31, 33, 34, 39, 41, 42, 44, 45, 46, 47, 50, 51, 54, 57, 58, 59, 61, 66, 67, 69, 70, 71, 73, 74, 75, 76, 77, 78, 79, 80, 97], "oblig": [84, 97], "obtain": [44, 47, 86, 88, 107, 110], "obviou": 85, "occur": [33, 78], "occurr": 79, "off": [47, 88, 91, 92, 102, 103, 107, 111], "offens": 84, "offer": 97, "offici": [84, 89, 95], "offlin": 84, "offset": [16, 20, 33], "oflabel": 105, "often": 86, "old": 76, "older": [85, 89], "omgwtfssl": 94, "omit": [87, 94], "onc": [85, 87, 89, 94], "one": [23, 30, 33, 34, 42, 47, 48, 54, 56, 70, 79, 85, 86, 87, 88, 89, 90, 92, 94, 97, 99, 100, 103, 110], "one_hot": 30, "ones": [34, 78, 87, 88, 94, 96, 110], "onli": [14, 23, 33, 34, 38, 39, 42, 47, 63, 70, 78, 83, 85, 86, 87, 88, 92, 94, 96, 97, 98, 100, 102, 103, 105, 107, 109, 110, 111], "onlin": [61, 84], "onto": 85, "op": [24, 30, 43, 47, 56], "opac": 92, "open": [84, 85, 86, 89, 96], "openmp": [88, 110], "oper": [22, 24, 33, 43, 45, 47, 66, 78, 86, 89, 100, 102, 103, 107], "oppos": [56, 90], "opt": [89, 94, 102, 106], "optic": [34, 83], "optim": [26, 28, 49, 53, 54, 87, 92, 96, 99, 100, 112], "optimizing_method": 106, "option": [14, 19, 20, 26, 29, 30, 31, 32, 33, 34, 39, 41, 42, 44, 45, 46, 47, 49, 50, 54, 56, 58, 59, 61, 62, 64, 65, 66, 67, 69, 70, 71, 73, 74, 75, 76, 77, 78, 79, 80, 83, 86, 87, 89, 94, 95, 96, 99, 100, 109, 110, 112], "option_pars": 66, "optional_path": 66, "options_pars": [33, 44, 45, 67, 69, 70, 71, 73, 75, 77, 78, 79], "orchestr": [87, 100], "order": [30, 33, 34, 39, 47, 58, 61, 70, 86, 87, 89, 92, 94, 102, 103, 107], "org": [25, 28, 83, 84, 88, 90, 96, 97, 104, 107, 109, 110, 111], "orient": [15, 33, 34, 62, 76, 84, 87, 88, 110], "orig": [34, 46, 50, 58, 66, 86, 88, 89, 91, 92, 98, 100, 102, 103, 105, 107, 110], "orig_data": [34, 35, 39, 46, 63], "orig_nam": [38, 50, 58, 66, 102, 103, 107], "orig_nu": [86, 87, 88, 91, 107, 110], "orig_zoom": [35, 39, 63, 64, 66], "origin": [24, 38, 39, 43, 46, 47, 54, 63, 64, 66, 67, 74, 85, 86, 91, 97, 102, 103, 105, 111], "ornt": 62, "other": [21, 33, 45, 47, 54, 84, 85, 86, 87, 89, 90, 91, 92, 94, 95, 97, 98, 99, 100, 110, 111], "other_mapp": 54, "otherfold": 100, "otherwis": [33, 47, 64, 66, 84, 97, 104, 110, 111], "our": [85, 87, 89, 90, 94, 95, 96, 98, 105, 110], "out": [20, 24, 39, 42, 43, 47, 50, 54, 59, 85, 96, 97, 103, 110], "out_affin": 33, "out_annot": 70, "out_block": [24, 43], "out_dir": [58, 66, 70, 102, 103, 107], "out_encod": [24, 43], "out_label_nam": 73, "out_r": [39, 64], "out_scal": [39, 64, 66], "out_shap": 33, "out_str": 59, "out_tensor_shap": [42, 65], "outannot": 70, "outaparc": 78, "outaparcnam": 79, "outblock": [24, 43], "outer": 34, "outlier": 30, "outp_block": [42, 65], "outpeform": 90, "output": [24, 30, 32, 34, 39, 41, 42, 43, 46, 47, 54, 56, 57, 61, 64, 65, 66, 70, 73, 75, 76, 78, 79, 80, 83, 85, 86, 87, 88, 89, 90, 92, 94, 95, 98, 99, 100, 102, 103, 109, 110, 111], "output_dir": 107, "output_s": 32, "output_seg_stat": 111, "output_transform": [30, 56], "outputdenseblock": [43, 65], "outputdir": 87, "outsid": [79, 86], "outstand": 97, "outsurf": 75, "over": [50, 56, 61, 64, 86, 87, 90, 99], "overal": [38, 105], "overdetermin": 68, "overestim": 86, "overlai": 91, "overrid": 106, "overview": [88, 95], "overwrit": [54, 70, 76, 86, 87, 94, 98], "overwritten": 111, "overwrot": [88, 102, 103, 107], "own": [14, 79, 85, 86, 89, 92, 94, 95, 97, 100, 104], "owner": 97, "ownership": 97, "p": [83, 88, 89, 96, 109], "p_dst": 68, "p_mov": 68, "packag": [61, 85, 88, 90, 94, 98, 109], "packet": 89, "pad": [20, 32, 35, 47, 66], "pad_siz": 32, "pad_size_imag": 32, "pad_size_mask": 32, "pad_slic": 47, "pad_typ": 32, "padded_s": [42, 65], "page": [89, 92, 94], "paint": 74, "paint_cc_into_pr": 81, "paint_in_cc": 74, "pair": [47, 50, 54, 68, 86], "palett": 54, "panda": [34, 47, 54, 111], "paper": [90, 107], "parallel": [34, 39, 47, 50, 85, 88, 90, 94, 95, 96, 100, 108, 109, 110], "parallel_seg": [99, 109], "parallel_surf": [90, 99, 109, 110], "param": [19, 20, 23, 24, 31, 38, 42, 43, 65], "paramet": [13, 14, 15, 19, 20, 21, 24, 25, 26, 28, 29, 30, 31, 33, 34, 35, 36, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 61, 62, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 87, 94, 99, 100, 111], "parcel": [34, 77, 78, 83, 91, 110], "parecl": 77, "parent": [61, 94], "pars": [25, 47, 61, 66, 71, 100], "parse_arg": [47, 58], "parse_build_fil": 61, "parse_fil": 47, "parse_vers": 71, "parser": [25, 33, 44, 45, 46, 47, 58, 61, 66, 67, 69, 70], "parser_default": 81, "part": [47, 83, 87, 88, 97, 100, 102, 110], "parti": 97, "partial": [14, 47, 83, 88, 91, 92, 96, 111], "partici": 90, "particip": [84, 90], "particular": [86, 91, 97], "partit": [87, 100], "partition_seg": 100, "partition_surf": 100, "pass": [30, 44, 47, 50, 54, 61, 63, 70, 73, 83, 87, 88, 89, 90, 91, 92, 98, 99, 100, 102, 103, 107, 109, 110, 111], "pat_is_bord": 47, "pat_is_nbr": 47, "pat_label_count": 47, "pat_label_sum": 47, "patch": [47, 111], "patch_corn": 47, "patch_filt": 47, "patch_neighbor": 47, "patch_siz": [13, 16, 47, 111], "patent": 97, "path": [13, 14, 26, 31, 34, 38, 46, 47, 49, 50, 52, 57, 58, 61, 64, 66, 69, 70, 73, 75, 76, 83, 86, 87, 88, 89, 90, 94, 98, 99, 100, 102, 103, 104, 105, 106, 107, 109, 110, 111], "path_hdf5_train": 106, "path_hdf5_val": 106, "path_to": 110, "path_to_t1": 87, "pathlik": [26, 39, 49], "patient": 96, "pattern": [18, 28, 38, 90, 100, 103, 105, 107], "paulcz": 94, "paulczar": 94, "pd": [34, 38, 47], "pdf": 57, "pem": 94, "peng": 107, "peopl": 85, "per": [23, 33, 42, 47, 56, 87, 88, 91, 99, 100, 111], "per_class": 30, "percent": 97, "percentil": [30, 47], "perform": [20, 28, 34, 39, 40, 47, 50, 54, 62, 65, 67, 83, 85, 86, 87, 88, 89, 90, 94, 96, 97, 99, 100, 107], "perman": 84, "permiss": [84, 96, 97], "permit": 90, "permut": 39, "permute_ord": 39, "perpetu": 97, "person": [84, 90], "pertain": 97, "phase": 28, "physic": 84, "pial": [91, 95], "pick": 98, "pip": [61, 88, 89, 94, 98], "pip3": 89, "pipe": [59, 99], "pipelin": [25, 46, 50, 83, 89, 90, 94, 95, 96, 98, 100, 101, 108, 109], "pipeline_conform_and_save_orig": 46, "pipeline_s": 50, "pixel": [20, 34], "pkl": [102, 103, 104, 107], "place": [87, 94, 97, 98], "placement": 95, "plan": 88, "plane": [15, 16, 38, 39, 46, 49, 58, 64, 66, 105, 106], "platform": [71, 85, 87, 94], "pleas": [81, 83, 85, 88, 89, 93, 96, 107, 109, 110, 111], "pledg": 95, "plexu": 44, "plot": [31, 34, 38, 57, 92], "plot_confusion_matrix": [31, 57], "plot_predict": [31, 57], "plt": [31, 57], "plt_titl": [31, 57], "plu": [47, 100], "plugin": [85, 94], "png": 107, "po": [32, 47], "point": [68, 81, 83, 85, 86, 87, 88, 89, 90, 94, 98, 109, 110], "pointer": 61, "polici": [28, 84, 95], "polit": 84, "pon": 86, "pool": [24, 34, 43, 46, 50, 59, 106, 109], "popen": [59, 61, 80], "popul": [96, 110], "posit": [14, 32, 33, 40, 42, 45, 47, 48, 56, 65, 84, 86], "posixpath": 49, "possibl": [54, 85, 89, 93, 94, 95, 97, 105, 107, 109, 111], "possibli": 85, "post": [39, 84], "post_prediction_mapping_hook": 39, "potenti": [50, 85, 90, 94, 98], "power": [87, 90, 97, 99], "powershel": 89, "ppa": 89, "practic": [95, 110], "pre": [38, 89, 92, 94, 105, 107], "prebuild": 94, "preced": 34, "precis": 56, "precision_recal": 56, "pred": [29, 30, 55, 74], "pred_batch": 29, "pred_cl": 56, "pred_class": 66, "pred_nam": [58, 102, 103, 107, 111], "pred_prob": [39, 64], "predict": [15, 22, 23, 29, 30, 31, 34, 39, 42, 43, 46, 54, 56, 57, 62, 64, 66, 88, 103, 105, 106, 107, 110], "prediction_sag": [15, 34, 62], "prediction_visu": 29, "prefer": [61, 85, 89, 90, 91, 92, 94, 97, 98], "prefer_cach": 61, "prefix": [34, 58, 89], "prelu": [24, 43], "prepar": [16, 66, 87, 88, 90, 97], "prepare_checkpoint": 66, "prepend": [99, 110], "preproc_imag": 47, "preprocess": 47, "present": [34, 38, 91], "presurf": 86, "pretess": 75, "pretess127": 75, "prev": [24, 43], "previou": [24, 39, 43, 85, 90, 99, 100], "primari": [47, 86, 91, 103], "primarili": 86, "primary_slic": 16, "print": [31, 33, 50, 58, 61, 70, 88, 99, 100, 109, 110], "print_build_fil": 61, "prior": [14, 86], "prior_model_path": [26, 49], "privat": 84, "pro": [89, 94], "probabl": [39, 64, 66], "problem": [85, 89], "procedur": [85, 92], "process": [16, 19, 22, 24, 30, 34, 35, 38, 43, 46, 50, 56, 60, 61, 63, 64, 66, 85, 88, 89, 91, 92, 94, 95, 96, 100, 102, 103, 105, 109, 110, 111], "process_funct": [30, 56], "produc": [79, 86, 87, 89, 92, 96, 110], "product": 97, "profession": 84, "prog": 47, "program": [88, 92, 102, 103, 107, 110], "progress": [29, 99], "project": [61, 83, 84, 85, 88, 94, 96, 110], "project_fil": 61, "project_root": 61, "projmm": 78, "promin": 97, "propag": [65, 86], "properli": [75, 107], "properti": [16, 40, 46, 48, 50, 54, 99], "protocol": 96, "proven": 95, "provid": [14, 29, 34, 48, 50, 54, 59, 65, 66, 83, 85, 86, 87, 88, 89, 90, 94, 96, 97, 106, 110], "pth": 64, "pub": 92, "public": [83, 84, 88, 96, 109, 110], "publicli": 97, "publish": [84, 98], "pull": [85, 87, 89, 95, 110], "purpos": [96, 97], "push": [85, 94], "put": [32, 99, 105], "pv": [47, 111], "pv_calc": 47, "pv_calc_patch": 47, "pv_guid": 47, "pv_stat": 47, "pvfile": [47, 111], "pvmeasur": 47, "pvstat": 47, "pwd": [89, 92, 100], "py": [46, 88, 89, 94, 98, 101, 108, 109, 110, 112], "py38_4": 89, "pydata": 111, "pypackag": 61, "pyplot": 31, "pypopen": 59, "pyproject": [61, 94], "python": [33, 54, 61, 88, 92, 94, 98, 103, 106, 107, 109, 110, 111], "python3": [88, 89, 103, 106, 109, 110], "python_cmd": [88, 109, 110], "pythonpath": [89, 94], "pytorch": [17, 28, 36, 50], "pytorch_enable_mps_fallback": 89, "qatool": 92, "qc": [66, 88, 89, 103, 107], "qc_log": 103, "qc_snap": [88, 107], "qc_snapshot": [66, 88, 107], "qform": 33, "qo": [89, 94], "qsphere": [88, 110], "quadrat": [33, 34], "quadro": 92, "qualiti": [86, 92, 96, 107, 110], "quanti": 96, "quantifi": 90, "question": [84, 108], "queue": 99, "quick": [93, 94, 95], "quick_qc": 81, "quickli": 94, "quit": 92, "quot": [48, 100], "r": [34, 54, 68, 73, 77, 85, 89, 90, 105], "ra": [15, 33, 34, 69, 73], "race": 84, "radeon": [89, 94], "radiu": [21, 67, 73, 78], "rais": [20, 34, 41, 47, 48, 49, 50, 53, 54, 58, 65, 66, 67, 68, 70, 72, 73], "ram": 89, "ran": [47, 99, 110], "random": [14, 32, 106], "randomaffin": 14, "randombiasfield": 14, "randomflip": 14, "randomlabelstoimag": 14, "randomli": 32, "rang": [33, 47, 62, 67], "rank": 30, "rare": 86, "ras2ra": [33, 69], "rate": [28, 29, 53, 55, 106], "raw": [54, 89, 99, 100], "re": [33, 34, 46, 47, 83, 85, 86], "reachabl": 49, "read": [20, 34, 47, 59, 61, 67, 70, 71, 78, 79, 85, 88, 111], "read_and_close_vers": 61, "read_annot": 78, "read_classes_from_lut": 34, "read_colort": [70, 71], "read_geometri": 78, "read_lta": 20, "read_multiple_label": 70, "read_talairach_xfm": 67, "read_version_from_project_fil": 61, "readabl": 97, "readi": 89, "readm": [83, 89, 94, 96], "real": 30, "realist": 102, "realli": [85, 86, 92, 96], "reason": [25, 84, 85, 96, 97], "reassign": 54, "rebas": 85, "recal": 56, "receiv": [24, 43, 50, 97], "recent": [89, 110], "recipi": 97, "recogn": 33, "recommend": [83, 86, 87, 88, 89, 90, 91, 94, 96, 100, 102, 103, 107, 110], "recon": [83, 85, 86, 88, 89, 91, 92, 94, 96, 99, 100, 101, 108], "recon_surf": [81, 89, 94, 110], "reconstruct": [87, 88, 94, 99, 100, 109, 110], "reconstructioni": 109, "record": [104, 107], "recreat": 85, "redistribut": 97, "reduc": [34, 41, 45, 54, 85, 90, 92, 103], "reduce_to_aseg": 81, "reducelronplateau": [28, 106], "reducelronplateauwithrestart": 28, "reduct": 41, "ref_img": 62, "refer": [20, 25, 28, 30, 47, 62, 75, 88, 91, 95, 109, 110], "referenc": 47, "reflect": 32, "reg": [70, 73, 88], "reg_mod": [66, 83, 88, 107], "regard": [84, 97], "regardless": 84, "region": [20, 44, 47, 67, 78, 79, 102], "region_label": 44, "regist": [69, 83, 87, 88, 90, 91, 98, 107, 110], "registr": [66, 69, 87, 88, 90, 92, 95, 98, 107, 110], "registri": 94, "regroup": 14, "regular": [88, 90], "reject": 84, "rel": [49, 50, 58, 100, 111], "relabel": 15, "relat": [14, 44, 100], "releas": [34, 94, 98, 110], "relev": [33, 47, 85, 86, 88], "reliabl": [25, 83, 85, 88, 90, 96, 109], "religion": 84, "relu": [24, 43], "remain": [34, 97], "remap": [15, 34, 62], "remot": 85, "remov": [20, 34, 47, 48, 49, 78, 84, 87, 92, 94, 99, 102, 103, 105, 107, 111], "remove_ckpt": 49, "remove_suffix": [58, 102, 103], "renam": 76, "render": [92, 94], "reorder": 33, "reorient": [15, 33, 62], "reorient_img": 62, "repeat": 79, "repercuss": 84, "replac": [23, 34, 42, 58, 78, 86, 88, 89, 94, 98, 110, 111], "replace_label": 78, "replic": 47, "repo": [85, 89], "report": [84, 91, 95], "report_empti": 47, "repositori": [85, 89, 102, 107], "repres": [15, 38, 42, 43, 45, 49, 50, 65, 84, 90, 97, 99], "represent": 84, "repro": 85, "reproduc": [85, 97, 111], "reproduct": [85, 97], "request": [41, 42, 50, 65, 85, 86, 100, 102], "requir": [20, 33, 47, 50, 53, 70, 83, 86, 94, 95, 97, 99, 100, 103, 106, 109, 110, 111], "require_measurefil": 47, "require_pvfil": 47, "rerun": 100, "resafe_surfac": [75, 76], "resampl": [33, 83, 103], "rescal": [33, 62, 65, 66, 67], "rescale_imag": 62, "research": [83, 88, 96, 109, 110], "reserv": 89, "reset": [29, 30, 55, 56, 85], "resiz": [20, 65], "reslic": 33, "resolut": [14, 39, 63, 64, 66, 83, 88, 96, 107, 109, 110, 112], "resolv": [50, 85, 86, 93], "resourc": [87, 88, 89, 94, 98, 99, 100, 110], "respect": [30, 31, 40, 47, 56, 84, 87, 94, 100, 110], "respons": [93, 95, 97], "restart": 28, "result": [29, 30, 31, 33, 34, 41, 47, 50, 59, 66, 84, 86, 88, 89, 90, 91, 92, 96, 97, 102, 103, 107, 109, 110, 111], "result_path": 13, "resum": [26, 49], "resume_experi": [26, 49], "retain": [24, 43, 97], "retcod": 59, "retrain": 107, "retriev": [28, 50, 63], "return": [14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31, 33, 34, 35, 36, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53, 54, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 73, 74, 75, 76, 77, 78, 79, 80, 94], "return_bord": 20, "return_map": 47, "returncod": 80, "reus": [90, 110], "reuter": [83, 84, 88, 90, 96, 107, 109, 110], "rev_map": 73, "revers": 62, "reversed_dict": 54, "revert": 110, "review": 84, "revis": [97, 111], "rewrit": [75, 76, 85], "rewrite_mc_surfac": 81, "rewrite_oriented_surfac": 81, "rewritten": 76, "rgba": [54, 78], "rh": [34, 70, 86, 91, 105], "rhcerebralwhitematt": 111, "rhcortex": 111, "rhsurfacehol": 111, "ribbon": [88, 110], "right": [15, 21, 34, 38, 44, 53, 61, 69, 84, 87, 91, 97, 99, 105], "rigid": [68, 69], "risk": 97, "rm": [87, 89, 92, 94, 110], "rmat2angl": 68, "rmax": 34, "rmin": 34, "rng_seed": 106, "robust": [14, 33, 47, 66, 86, 88, 90, 107, 111], "robust_percentag": 47, "robust_voxel_count": 47, "robustli": [33, 90], "rocm": [89, 94], "roi": [16, 83, 110], "root": [49, 50, 58, 61, 87, 88, 94, 100], "rosa": [88, 90, 109], "rotat": [14, 68, 77, 107], "rotate_spher": 81, "round": 33, "row": [14, 47, 100], "royalti": 97, "rtx": 92, "run": [22, 25, 39, 46, 50, 61, 63, 64, 66, 80, 83, 85, 86, 89, 91, 92, 95, 96, 98, 99, 102, 103, 104, 106, 108, 110, 111], "run_fastsurf": [86, 87, 88, 89, 90, 92, 98, 99, 102, 103, 107, 109, 110], "run_model": [46, 108, 112], "run_predict": [81, 88, 94, 101, 108], "run_tool": [61, 81], "runmodelondata": 46, "runner": [49, 88, 102, 103, 106, 107, 109], "runtim": [59, 85], "runtimeerror": [20, 34, 47, 50, 54, 58, 66], "rusiel": 90, "sabuncu": 90, "safe": [88, 94], "sag_mask": 105, "sagitt": [15, 34, 38, 39, 46, 62, 66, 102, 103, 105, 106, 107], "sagittal_coronal_remap_lookup": 34, "sagittal_lut_dict": 34, "sai": 100, "same": [14, 15, 20, 23, 30, 42, 47, 54, 61, 70, 73, 78, 80, 85, 86, 87, 88, 89, 90, 92, 94, 99, 100, 102, 103, 106, 107, 110, 111], "sampl": [14, 32, 78], "sample_img": 78, "sample_intensity_stats_from_imag": 14, "sample_nearest_nonzero": 78, "sample_parc": 81, "santiago": 107, "save": [13, 21, 26, 31, 34, 46, 49, 57, 72, 75, 79, 86, 87, 88, 90, 98, 102, 103, 107, 110, 111], "save_a": [34, 46], "save_checkpoint": [26, 49], "save_imag": 34, "save_img": 46, "save_mgh_imag": 21, "save_nii_imag": 13, "save_path": [13, 21], "sbom": 94, "scale": [14, 33, 39, 42, 63, 64, 65, 66, 106, 111], "scale_factor": [42, 65], "scale_factor_out": [42, 65], "scalecrop": 33, "scan": 14, "scanner": 96, "scannerra": 75, "scenario": [92, 111], "scene": 95, "schedul": [26, 28, 49, 53, 87, 99, 100, 106], "schedular": 53, "scheme": [86, 107], "schmanski": [88, 90, 109], "scipi": 30, "scope": [85, 95], "score": [29, 30, 55, 56], "screen": 94, "script": [25, 33, 46, 47, 61, 85, 86, 87, 88, 89, 90, 91, 94, 96, 98, 99, 100, 102, 103, 104, 106, 107, 109, 110, 111], "sd": [86, 87, 88, 89, 90, 92, 94, 98, 99, 100, 102, 103, 107, 109, 110, 111], "sdir": [88, 110], "sdk": 85, "se": [102, 103], "search": [26, 41, 47, 49, 50, 61, 78, 85, 88, 100, 102, 103, 109], "search_pattern": 38, "search_tag": [58, 102, 103], "sec": 92, "seccomp": [89, 94], "second": [14, 50, 59, 65, 86, 87, 89, 92, 100, 102, 103, 107, 111], "secondari": 86, "section": [61, 85, 88, 90, 92, 97], "secur": [89, 94, 95], "see": [44, 61, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 94, 96, 98, 99, 100, 102, 103, 106, 109, 110], "seed": [14, 86, 106], "seem": [85, 89], "seg": [47, 69, 78, 83, 87, 88, 91, 100, 103, 107], "seg_": 100, "seg_arrai": 44, "seg_bord": 47, "seg_dst": 69, "seg_input": 88, "seg_log": [88, 102, 103, 107], "seg_mean": [47, 111], "seg_mov": 69, "seg_onli": [83, 86, 87, 88, 89, 90, 91, 92, 100, 109, 110], "seg_output": 88, "segdir": 110, "segemnt": [88, 109], "segfil": [47, 50, 111], "segid": 47, "segmap": 21, "segment": [14, 15, 23, 25, 29, 30, 33, 34, 38, 42, 44, 45, 46, 47, 50, 66, 67, 69, 74, 89, 90, 94, 95, 96, 98, 99, 100, 102, 103, 105, 106, 107, 109, 110, 111], "segstat": [81, 101, 108], "segstatsfil": [47, 111], "select": [21, 66, 69, 83, 88, 91, 94, 100, 102, 103, 106, 107, 111], "self": 94, "sell": 97, "semi": [43, 89], "send": [80, 100], "sensit": [90, 96], "sensitivii": 90, "sent": [94, 97], "separ": [47, 54, 71, 84, 87, 97, 99, 100], "sequenc": [14, 20, 30, 47, 54, 96], "sequenti": [34, 87, 88, 109], "seri": [99, 110], "serial": [50, 100], "serialexecutor": 50, "serv": 47, "server": 49, "servic": 97, "set": [16, 28, 30, 31, 33, 34, 38, 39, 46, 50, 52, 54, 56, 57, 62, 64, 65, 66, 68, 75, 76, 79, 84, 87, 88, 89, 92, 98, 99, 102, 103, 105, 106, 107, 109, 110, 111], "set_and_create_outdir": 46, "set_cfg": [39, 64], "set_devic": [30, 56], "set_lr": 28, "set_model": [46, 64], "set_plan": 16, "set_subject": 46, "set_summary_path": 31, "set_up_cfg": [46, 66], "set_up_model_param": 46, "setter": 46, "setup": [86, 88, 89, 90], "setup_log": 52, "setup_model": [39, 64], "setup_opt": [25, 80], "setupfreesurf": [86, 87, 90, 110], "sever": [87, 94, 96], "sex": 84, "sexual": 84, "sform": 33, "sgd": 106, "sh": [86, 87, 88, 89, 90, 92, 94, 98, 101, 102, 103, 107, 108], "shall": [96, 97], "shape": [15, 20, 33, 41, 42, 47, 65, 66, 68, 78, 79], "share": [14, 47, 50, 97], "shell": 94, "shift": 33, "shm": 89, "should": [14, 15, 20, 30, 33, 34, 45, 47, 56, 57, 58, 61, 64, 65, 68, 69, 70, 71, 79, 85, 86, 87, 88, 89, 94, 96, 98, 100, 102, 103, 105, 107, 111], "show": [84, 85], "shown": 91, "shrink": 67, "shrunk": 47, "sid": [58, 66, 73, 86, 87, 88, 89, 90, 92, 94, 98, 99, 100, 102, 103, 107, 109, 110, 111], "side": [20, 85, 95], "sif": [87, 89, 90, 92, 98, 100, 110], "sigma": 43, "sign": 94, "signatur": [30, 56], "significantli": 87, "silicon": [88, 89, 94], "similar": [14, 30, 33, 47, 59, 86, 88, 89, 90, 99, 102, 103, 110], "similarli": [13, 85, 89, 94], "simpl": 47, "simpler": 45, "simpli": [85, 92, 94, 98], "simplifi": [87, 88, 91, 107, 110], "sinc": [85, 88, 89, 94, 98, 102, 103], "singl": [16, 30, 39, 48, 64, 87, 94, 96, 102, 107, 111, 112], "singular": [90, 95, 96, 99, 100], "singularity_imag": [87, 100], "site": 49, "sitk": [67, 69], "situat": [90, 102, 107], "six_connect": 47, "size": [14, 20, 31, 32, 33, 34, 38, 39, 46, 47, 48, 50, 64, 66, 73, 84, 86, 88, 89, 92, 102, 103, 105, 106, 107, 109, 110, 111], "size_averag": 41, "skip": [23, 24, 42, 43, 47, 61, 83, 86, 88, 99, 100, 107, 110], "skip_cleanup": 100, "skull": [86, 90], "slice": [15, 16, 20, 23, 33, 34, 38, 42, 47, 69, 88, 105, 106], "slice_lia2ra": 15, "slice_ras2lia": 15, "slice_thick": [16, 34, 38], "slicer": 47, "slicer_large_patch": 47, "slicer_large_to_patch": 47, "slicer_large_to_smal": 47, "slicer_patch": 47, "slicer_small_to_patch": 47, "slicingsequ": 47, "slicingtupl": 47, "slide": 94, "slightli": [30, 90], "slow": [89, 102, 103, 107], "slower": [88, 89, 92, 96], "slurm": [95, 99, 108], "slurm_array_task_count": 99, "slurm_array_task_id": 99, "slurm_jobarrai": 100, "slurm_task_id": 99, "small": [30, 33, 34, 47, 85, 86, 87, 92, 110], "smaller": [21, 33, 44, 79, 88, 90, 94, 100, 111], "smallest": [33, 88, 111], "smooth": [78, 79, 90], "smooth_aparc": 81, "smoothed_label": 79, "snapshot": [66, 88, 107], "snapshott": 94, "snippet": 100, "so": [15, 20, 26, 34, 49, 50, 58, 67, 70, 73, 79, 85, 87, 88, 89, 91, 92, 94, 96, 98, 99, 100, 110], "social": 84, "socioeconom": 84, "softmax": 65, "softwar": [89, 91, 94, 96, 97], "sole": [85, 97], "solut": [68, 83, 88, 94, 96, 109, 110], "solv": [85, 89], "some": [85, 86, 89, 91, 94, 95, 110], "somefold": 100, "someon": 85, "sometim": [33, 86], "sourc": [13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 86, 87, 88, 89, 90, 94, 96, 97, 103, 106, 107, 110], "source_intens": 67, "source_shap": 16, "source_spac": 54, "space": [15, 20, 30, 33, 34, 47, 54, 62, 67, 69, 78, 84, 87, 88, 90, 109, 111], "spars": [78, 79], "spatial": [23, 42], "spatialimag": [33, 34, 46, 47], "spatiotempor": 90, "spec": 89, "special": [97, 102], "specif": [20, 30, 33, 38, 39, 47, 49, 56, 84, 86, 87, 88, 91, 94, 96, 98, 99, 100, 102, 103, 105, 107, 110], "specifi": [14, 20, 28, 30, 33, 46, 47, 54, 65, 66, 70, 87, 88, 94, 98, 99, 102, 103, 104, 106, 107, 110, 111], "spectral": [88, 110], "speed": [87, 88, 92, 102, 103, 107, 110], "sphere": [21, 70, 73, 77, 88], "spheric": [21, 88, 90, 110], "spherical_wrapp": 80, "spherically_project_wrapp": 81, "split": [31, 34, 99], "split_cortex_label": 34, "splot": 34, "spm": 86, "sqr": 47, "sqrt": 47, "squar": [47, 68], "squeue": 100, "src": [33, 49, 69, 70, 73, 88, 102, 103, 106, 107, 109], "src_dir": 70, "src_fname": 72, "src_header": 72, "src_label": 70, "src_label_nam": 73, "src_min": 33, "src_sphere": 73, "src_sphere_nam": 70, "srcsphere": 70, "srun_fastsurf": [87, 108], "ssl": 94, "stabil": 47, "stabl": [28, 30, 85, 87, 89], "stack": [20, 34, 85], "stage": [28, 86], "stai": [58, 73, 83, 96], "standard": [26, 32, 33, 49, 63, 88, 94, 95, 100, 102, 103, 107, 110], "start": [41, 47, 87, 89, 94, 95, 96, 99, 100, 110], "startup": [92, 99], "stat": [14, 29, 47, 86, 87, 88, 90, 91, 92, 96, 102, 107, 110, 111], "state": [26, 30, 49, 64, 97, 100], "statement": 97, "statist": [14, 47, 55, 83, 87, 88, 89, 91, 92, 95, 96, 107, 110, 111], "statsfield": 102, "statsfil": 92, "statu": [61, 84, 88, 100], "statusfil": 99, "std": [14, 32], "stddev": 47, "stderr": 59, "stdin": 99, "stdout": [33, 34, 59, 61, 94, 103], "step": [28, 29, 57, 85, 86, 87, 88, 89, 90, 100], "step_lr": 106, "steplr": 53, "still": [90, 110], "stool": [99, 100], "stop": [34, 70, 87], "stop_miss": 70, "stoppag": 97, "storag": [94, 100], "store": [18, 19, 20, 47, 66, 73, 87, 88, 89, 102, 103, 107, 110], "store_talairach": [18, 19], "store_tru": 58, "str": [13, 15, 19, 20, 25, 26, 30, 31, 32, 34, 36, 38, 39, 46, 47, 48, 49, 50, 51, 52, 54, 56, 57, 58, 61, 63, 64, 65, 66, 67, 70, 71, 72, 73, 75, 76, 78, 79, 80, 88, 103], "strand": [34, 38, 105], "strategi": [14, 20], "stream": [88, 90, 92, 96], "strenght": 96, "strict": 33, "strictli": 14, "stride": 106, "stride_conv": [24, 43, 106], "stride_pool": [24, 43, 106], "string": [15, 33, 34, 39, 47, 48, 50, 61, 66, 70, 71, 73, 94, 100], "strip": [86, 90, 103], "strong": [85, 86], "strongli": 94, "structnam": 47, "structur": [14, 34, 47, 83, 86, 88, 90, 91, 96, 107, 109, 110, 111], "stub": 102, "studi": [90, 99, 100], "style": [34, 61, 88, 103, 105, 110], "sub": [25, 26, 47, 49, 83, 88, 91, 92, 96, 100, 102, 103, 107, 109], "sub_modul": 81, "sub_patch": 47, "sub_region": 47, "subcort": [86, 91], "subcortgrai": 111, "subdirectori": 100, "subfield": [96, 107], "subfold": [86, 96, 110], "subject": [16, 19, 35, 38, 46, 47, 50, 64, 66, 70, 73, 88, 90, 94, 95, 97, 98, 100, 102, 105, 107, 108, 109, 111], "subject1": 87, "subject10": 87, "subject2": 87, "subject3": 87, "subject_dir": [38, 50, 86], "subject_id": [47, 99, 100, 110, 111], "subject_id1": [87, 100], "subject_list": [87, 99, 100, 110], "subject_list_awk_code_arg": 100, "subject_list_awk_code_sid": 100, "subject_list_awk_code_t1": 100, "subject_list_delim": 100, "subject_nam": [63, 64, 66], "subject_path": 16, "subject_success": 100, "subjectdataset": 16, "subjectdirectori": [46, 50], "subjectdirectoryconfig": 58, "subjectid": [88, 110], "subjectlist": [46, 50, 58], "subjectload": 19, "subjects_dir": [47, 86, 88, 90, 109, 110, 111], "subjects_list": [18, 87, 110], "subjectx": [89, 94, 95, 98, 103], "subjid": 85, "sublicens": 97, "submiss": 97, "submit": [34, 50, 97, 100], "subpars": 111, "subparser_callback": 47, "subpatch": 47, "subprocess": 59, "subregion": 47, "subseg": [20, 62], "subsegment": 83, "subsequ": 97, "subset": [85, 87], "substitut": 88, "substructur": 83, "subtl": 90, "subtract": 20, "succe": 100, "succeed": [34, 38, 105], "success": [25, 47, 61, 66, 86, 87, 94, 99], "successfulli": [89, 99, 100], "sudo": 89, "sudr": 14, "suffici": [89, 99], "suffix": [34, 50, 88, 102, 103, 105, 107, 110, 111], "suggest": 95, "suitabl": 33, "sulci": [34, 38, 105], "sulcu": 34, "sum": [47, 56], "sum_of_intens": 47, "sum_of_intensity_squar": 47, "summari": [29, 31, 55, 91, 111], "sums_of_squar": 47, "super": 92, "supersed": 97, "suppli": 30, "support": [34, 47, 53, 58, 65, 83, 86, 88, 95, 96, 97, 99, 102, 109, 110], "supported_output_file_format": 34, "supratentori": 111, "supratentorialnotv": 111, "supratentorialnotventvox": 111, "sure": [75, 85, 87, 89, 94, 98, 110], "surf": [73, 78, 79, 83, 85, 86, 87, 88, 89, 91, 92, 94, 96, 100, 101, 108], "surf_": 100, "surf_ctab": 78, "surf_label": 78, "surf_lut": 78, "surf_nam": 78, "surf_onli": [83, 86, 88, 90, 100, 109, 110], "surf_xxx_yi": 100, "surf_xxx_yy_zz": 100, "surfac": [30, 70, 73, 75, 76, 78, 79, 87, 89, 90, 92, 94, 95, 96, 98, 99, 100, 101, 108, 109], "surface_backup": 76, "surface_fil": 76, "surfacehol": 111, "surfacera": 75, "surfer": [86, 87, 88, 92, 98, 110], "surflut": 78, "surviv": 90, "switch": [85, 88, 91, 92, 96, 98, 110], "symbol": 91, "symlink": [86, 91, 96], "symmetr": [30, 78, 79], "synchron": 46, "sys_ptrac": 89, "system": [68, 87, 94, 95, 97, 98, 99, 102, 103, 107, 110], "systemat": 86, "t": [14, 68, 69, 72, 85, 87, 89, 92, 103, 110], "t1": [13, 39, 63, 66, 86, 87, 88, 89, 90, 92, 94, 96, 98, 99, 100, 102, 103, 107, 109, 110, 111], "t1_1": [90, 109], "t1_2": [90, 109], "t1_input": [88, 110], "t1_path": [66, 100], "t1t2": [63, 64, 66], "t1w": [83, 88, 90, 99, 100, 107], "t2": [63, 66, 83, 88, 91, 99, 107, 109], "t2_input": 88, "t2_nu": 91, "t2_nu_reg": 91, "t2_path": 66, "t2tot1": 107, "t2w": [83, 99, 107], "t_0": 28, "t_addarg": 58, "t_mult": 28, "t_othervalu": 54, "tab": 54, "tabl": [20, 34, 47, 62, 73, 78, 91, 103, 105, 111], "table_to_datafram": 47, "tabular": 91, "tag": [85, 89, 94, 98, 102, 103], "tag_nam": 94, "take": [14, 65, 75, 76, 84, 87, 88, 92, 94, 109, 110], "taken": [70, 73, 88, 90], "tal": 67, "tal_reg": [88, 92], "talairach": [19, 67, 87, 88, 92, 95, 98, 110], "talk": 85, "target": [15, 20, 33, 41, 54, 66, 67, 69, 70, 73, 85, 88, 94, 99, 110], "target_bg": 67, "target_dtyp": 48, "target_img_s": 20, "target_intens": 67, "target_shap": [16, 20, 40, 66], "target_slic": 47, "target_spac": 54, "target_wm": 67, "targetdir": 110, "team": [84, 85], "tech": 94, "technic": 86, "tell": [87, 88, 96, 98], "temp": 57, "temp_competit": 103, "templat": [88, 90, 109, 110], "templateid": [90, 109], "tempor": 90, "temporari": 84, "temporarili": 84, "tensor": [14, 20, 23, 24, 29, 30, 32, 34, 39, 40, 41, 42, 43, 45, 46, 47, 55, 56, 57, 63, 64, 65, 66], "term": 97, "termin": [59, 88, 89, 97, 100, 110], "test": [17, 36, 50, 85, 87, 88, 89, 92, 94, 96, 110], "test_subject": [88, 107], "test_subject_t1": 88, "test_subject_t1_bias_field_correct": 107, "test_subject_t2_bias_field_correct": 107, "test_subject_t2_bias_field_corrected_and_coregistered_to_t1": 107, "testload": 16, "testmet": 29, "text": [47, 50, 58, 61, 88, 91, 92, 97, 108], "textio": 61, "th": [34, 99], "thalamu": 96, "than": [33, 44, 48, 68, 87, 88, 89, 92, 94, 99, 100, 111], "thank": [86, 93], "thei": [66, 73, 84, 85, 87, 94, 98, 107], "them": [66, 86, 87, 89, 96, 99, 104, 110], "theoret": 90, "theori": 97, "therapi": 90, "therebi": 75, "therefor": [30, 86, 90, 94, 96, 99, 107], "therein": 61, "thereof": 97, "thi": [14, 15, 20, 25, 26, 30, 31, 33, 34, 38, 39, 44, 45, 46, 47, 49, 50, 54, 56, 58, 61, 62, 64, 65, 66, 74, 75, 78, 79, 81, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 94, 96, 97, 98, 99, 100, 102, 103, 104, 105, 107, 109, 110, 111], "thick": [15, 34, 83, 86, 88, 90, 91, 92, 96, 105, 106, 110], "thick_slic": 15, "thing": [85, 89], "think": 96, "third": 97, "thoroughli": [89, 96], "those": [85, 86, 94, 96, 97, 98], "thousandth": 33, "thre": [44, 67], "thread": [22, 46, 47, 50, 64, 66, 81, 86, 87, 88, 94, 99, 102, 103, 107, 110, 111], "threadpoolexecutor": [34, 59], "threads_seg": [88, 99], "threads_surf": [88, 99], "threaten": 84, "three": [33, 34, 87, 91, 99, 100], "thresh": 70, "threshold": [15, 20, 33, 34, 38, 44, 46, 47, 67, 103, 105], "through": [33, 42, 43, 65, 85, 89, 90, 94, 97, 99, 106], "throughout": 83, "thu": [33, 94], "tid": [90, 109], "tid1": [90, 109], "tid2": [90, 109], "tidn": 90, "time": [34, 61, 83, 85, 86, 87, 88, 89, 90, 92, 94, 99, 100, 109, 110], "time_seg": 100, "time_surf": 100, "timelimit": 100, "timeout": [50, 59], "titan": 92, "titl": [31, 57, 85, 93, 97], "tl": 94, "tmp": 86, "tmult": 28, "to_same_typ": 54, "toch": 39, "togeth": [59, 99], "toml": [61, 94], "tool": [86, 90, 96, 99, 100, 102], "toolbox": 90, "toolchain": 89, "toolkit": 89, "top": [34, 47, 92, 110], "top_left": [32, 40, 65], "top_right": 65, "torch": [20, 26, 28, 29, 30, 34, 36, 39, 41, 45, 46, 49, 50, 53, 55, 56, 57, 63, 64, 65], "torchio": 14, "tort": 97, "total": [14, 41, 44, 55, 60, 86, 88, 92, 100, 102, 103, 107], "total_epoch": [29, 55], "total_it": [29, 55], "total_thread": 99, "totalgrai": 111, "totensor": [14, 32], "totensortest": [14, 32], "toward": [20, 24, 43, 84], "tp": [56, 57], "tpid": [90, 109], "tqdm": 99, "tqdm_disabl": 99, "trace": 85, "traceback": 85, "track": [46, 55, 85, 97], "tracker": 85, "tract": 83, "tracula": 96, "trade": [94, 97], "trademark": 97, "tradit": [83, 110], "trail": 48, "train": [17, 26, 28, 29, 36, 49, 55, 57, 88, 102, 105, 112], "training_sagittal_single_resolut": 106, "trajectori": 28, "transfer": [97, 98, 99], "transform": [14, 15, 16, 20, 30, 34, 35, 38, 54, 56, 62, 63, 66, 67, 68, 69, 72, 86, 87, 97, 107], "transform_axi": [15, 34], "transform_axial2coron": 62, "transform_axial2sagitt": [15, 62], "transform_coron": 15, "transform_sagitt": [15, 34], "transit": 83, "translat": [14, 97, 106], "transpos": [23, 42], "travers": 94, "treat": [47, 90], "tree": 73, "trg": [33, 69, 70, 73], "trg_label": 73, "trg_sid": [70, 73], "trg_sphere": 73, "trg_sphere_nam": 70, "trg_surf": 73, "trg_valu": 73, "trg_white": 70, "trg_white_nam": 70, "trgsphere": 70, "tri": [60, 90], "tria": [78, 79], "triangl": [76, 78, 79], "trick": 94, "trigger": 47, "troll": 84, "true": [14, 15, 24, 33, 34, 43, 47, 54, 56, 62, 69, 70, 71, 79, 94, 106], "true_cl": 56, "truth": [29, 34, 38, 56, 105], "try": [50, 85, 89, 96, 99, 110], "tsqrt": 69, "tsv": [54, 103, 105], "tsvlookupt": 54, "tune": [26, 49, 83, 91, 96], "tupl": [13, 16, 30, 31, 32, 33, 34, 39, 46, 47, 54, 56, 64, 65, 66, 67, 71, 73, 78], "turn": [33, 38, 105], "tutori": 86, "tutorial_data": 92, "tutorial_subj": 92, "twice": 89, "twitter": [83, 96], "two": [30, 32, 47, 65, 68, 83, 89, 90, 91, 94, 99, 100], "txt": [44, 87, 88, 89, 90, 94, 98, 103, 106, 110], "type": [15, 20, 30, 32, 33, 34, 46, 47, 48, 49, 54, 58, 78, 85, 94, 97, 107, 110], "type_hint": 54, "typeerror": 20, "typic": [47, 88], "u": [83, 85, 87, 89, 92, 94, 96, 100, 110], "uchar": [33, 34, 88, 110], "uint8": 33, "unaccept": 84, "unbias": [88, 90, 109], "unchang": 99, "unconfin": [89, 94], "undefin": [54, 86], "under": [34, 86, 87, 88, 89, 92, 94, 97, 98, 102, 103, 110], "underneath": 99, "undersegment": 86, "understand": [85, 86], "understood": 90, "undesir": [88, 109], "undetermin": 34, "undo": 47, "ungrow": 47, "unifi": 35, "uniform": 47, "uniform_filt": 47, "unify_img": 35, "unify_lateralized_label": 34, "union": [26, 30, 32, 33, 34, 39, 46, 47, 48, 49, 53, 56, 58, 70, 73, 97], "uniqu": 111, "unit": [30, 47, 111], "uniti": 30, "univari": 90, "universal_newlin": 59, "unknown": [21, 34, 71, 78], "unknown_label": 34, "unknown_mask": 21, "unless": [91, 94, 97, 99], "unlik": 33, "unlimit": 59, "unpool": [23, 24, 42, 43], "unquot": 48, "unquote_str": 48, "unreli": [86, 96], "unsid": 79, "unsuccess": 100, "until": [46, 85, 90, 100], "unwelcom": 84, "up": [20, 33, 34, 39, 42, 43, 46, 52, 62, 64, 65, 66, 78, 83, 85, 87, 88, 92, 100, 102, 103, 107, 110], "updat": [21, 28, 29, 30, 31, 39, 47, 54, 55, 56, 57, 64, 83, 85, 86, 89, 91, 93, 96, 100], "update_num_step": 57, "update_results_dir": 31, "update_split_path": 31, "update_stat": [29, 55], "update_structnam": 47, "upgrad": 89, "upinterpol": 43, "upon": [25, 107], "upright": 69, "upstream": 85, "url": [49, 66, 104], "us": [13, 14, 15, 20, 26, 28, 29, 30, 33, 34, 38, 39, 42, 46, 47, 49, 50, 54, 56, 58, 62, 64, 65, 66, 83, 84, 85, 87, 88, 89, 90, 91, 92, 93, 94, 95, 97, 98, 99, 100, 102, 103, 104, 105, 106, 107, 109, 110, 111], "usabl": 60, "usag": [30, 39, 46, 56, 88, 95, 102, 103, 104, 105, 106, 108, 111], "usecas": 94, "used_label": 47, "user": [50, 58, 85, 87, 88, 89, 90, 92, 94, 98, 100, 110], "usernam": 85, "usual": [15, 30, 59, 73, 78, 79, 85, 88, 90, 94, 98, 99, 110], "util": [36, 61, 81, 108], "v": [87, 89, 92, 94, 98, 110], "v0": 94, "v2": 94, "v5": 89, "v_dst": 77, "v_mov": 77, "val": [17, 36, 48], "val_load": [39, 64], "valid": [29, 31, 39, 48, 50, 55, 57, 61, 64, 87, 89, 96, 98, 99, 106], "validation_sagittal_single_resolut": 106, "valu": [14, 20, 26, 28, 29, 30, 33, 34, 39, 41, 44, 45, 46, 47, 48, 49, 50, 54, 55, 56, 57, 58, 61, 67, 69, 70, 73, 78, 79, 85, 86, 88, 94, 99, 105, 106, 111], "valueerror": [20, 47, 53, 54, 65, 66, 67, 68, 70, 72, 73], "var": [88, 94, 109, 110], "vari": 89, "variabl": [41, 87, 88, 89, 94, 98, 99, 109], "varianc": 90, "variou": [86, 89, 104], "vent_label": 44, "ventricl": [34, 44, 83], "ventriclechoroidvol": 111, "venv": 89, "verbal": 97, "verbos": [33, 70], "veri": [47, 86, 89, 90, 94, 96, 110, 111], "versa": [47, 62], "version": [33, 71, 81, 84, 85, 86, 87, 88, 91, 92, 94, 95, 97, 98, 99, 100, 107, 110], "version_lin": 61, "version_tag": 94, "versiondict": 61, "vertex": [47, 73, 75, 78, 79, 90, 91], "vertic": [73, 77, 78, 79], "vessel": 34, "vetric": 73, "via": [47, 70, 78, 79, 84, 85, 86, 88, 89, 90, 94, 95, 98, 100, 102, 103, 109, 110, 111], "vice": [47, 62], "video": [89, 94, 99], "vidx": 78, "view": [20, 23, 33, 39, 42, 64, 66, 88, 96, 102, 103, 107], "view_op": 46, "view_opt": 66, "viewagg_devic": [22, 46, 58, 64, 66, 88, 96, 99, 102, 103, 107], "viewer": 92, "viewgg_devic": 107, "viewoper": 66, "viewpoint": 84, "vinn": [63, 104, 110], "violat": 33, "virtual": [47, 111], "virtuallabel": 47, "visibl": [87, 94, 98, 110], "visual": [29, 89, 92, 96, 107], "visualize_batch": 31, "vol": [15, 34, 62], "volum": [14, 15, 20, 30, 34, 44, 47, 62, 66, 75, 78, 83, 86, 87, 88, 91, 92, 96, 102, 103, 111], "volume_mm3": 47, "volume_precis": [47, 111], "volume_similar": 30, "volumetr": 83, "vote": 79, "vox": 48, "vox2ra": 69, "vox2vox": 33, "vox_coord": 78, "vox_origin": 67, "vox_siz": [33, 34, 46, 48, 88, 100, 103], "vox_vol": 47, "voxel": [15, 20, 21, 33, 34, 38, 44, 47, 48, 67, 69, 78, 86, 88, 92, 103, 105, 110, 111], "voxel_count": 47, "voxels": 103, "voxelspac": 30, "voxsizeopt": [33, 34], "voxvol": 44, "vt": 54, "vulner": 95, "w": [15, 41, 42, 43, 86], "w6600": [89, 94], "wa": [14, 26, 38, 49, 50, 61, 75, 76, 84, 86, 87, 88, 89, 94, 97, 98, 100, 105], "wai": [33, 85, 87, 89, 90, 91, 92, 99, 100], "wait": [50, 59, 80, 90], "walk": 89, "want": [30, 47, 56, 85, 87, 89, 92, 98, 99, 110], "warm": 28, "warmup": 28, "warmup_factor": 28, "warmup_it": 28, "warmup_method": 28, "warmupcosinelr": 28, "warn": [34, 70, 81], "warp": 13, "warp_path": 13, "warranti": 97, "watersh": 86, "we": [14, 21, 33, 47, 50, 68, 70, 84, 85, 86, 88, 89, 90, 91, 92, 94, 96, 98, 99, 102, 103, 107, 110], "web": 85, "websit": [87, 98], "weigh": [63, 94], "weight": [13, 14, 15, 23, 31, 32, 34, 35, 38, 41, 42, 47, 63, 65, 87, 90, 92, 94, 96, 98, 100, 103, 105, 110], "weight_c": 41, "weight_dic": 41, "weight_factor": 65, "weight_vol": 34, "welcom": 84, "well": [47, 85, 86, 87, 88, 89, 90, 92, 94, 96, 99, 111], "were": [47, 91, 100], "wget": [89, 94], "whalf": 47, "what": [79, 84, 85, 87, 89, 95, 100], "when": [14, 20, 30, 33, 46, 65, 70, 78, 84, 87, 90, 94, 95, 98, 99, 102, 103, 107, 111], "whenev": 91, "where": [13, 14, 15, 20, 28, 29, 30, 45, 47, 54, 58, 62, 66, 69, 70, 73, 78, 79, 87, 88, 89, 90, 94, 97, 98, 99, 100, 102, 103, 107, 109], "wherev": 97, "whether": [14, 15, 19, 26, 33, 34, 44, 47, 48, 49, 50, 54, 61, 66, 70, 76, 85, 86, 88, 97, 100, 111], "which": [14, 21, 23, 28, 30, 33, 34, 42, 46, 47, 49, 58, 59, 61, 66, 70, 73, 78, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 94, 96, 97, 98, 99, 100, 102, 103, 105, 107, 110, 111], "while": [50, 58, 85, 86, 97, 100], "white": [14, 34, 45, 67, 70, 73, 91, 95], "white_check_mark": 93, "whitematteredits_freeview": 86, "who": [84, 94, 110], "whole": [46, 83, 86, 96, 97, 107, 110], "whom": 97, "whose": [44, 54, 106], "why": [85, 89, 94, 96, 98], "wide": 47, "wider": 79, "width": [13, 39, 42, 47, 64, 65, 69, 106], "wiki": 84, "window": [47, 85, 95], "wise": [31, 41, 83, 91, 110], "wish": 94, "withcc": 91, "within": [83, 84, 88, 90, 92, 94, 96, 97, 103, 106, 109, 110], "without": [34, 38, 48, 70, 81, 84, 86, 87, 91, 92, 94, 97, 99, 100, 105, 107], "wm": [21, 34, 38, 45, 67, 73, 83, 86, 88, 90, 105, 110], "wm_mask": 21, "wm_merge_clean": 81, "wmparc": [91, 96], "wo": 88, "won": 87, "work": [49, 50, 61, 86, 87, 88, 89, 90, 94, 96, 97, 98, 99, 100, 102, 103, 106, 107, 109, 110], "worker": 94, "workload": 87, "workstat": 92, "worldwid": 97, "would": [85, 86, 87, 89, 90, 92, 94, 98, 100], "wrapper": 110, "write": [29, 34, 47, 55, 61, 70, 72, 73, 85, 87, 97, 99, 111], "write_annot": 70, "write_statsfil": 47, "write_summari": [29, 55], "writelta": 72, "writer": [29, 55], "writesurflabel": 73, "written": [70, 73, 87, 94, 97, 98, 102, 103, 107, 111], "wsl": 89, "wsl2": 89, "wt1": 63, "wt2": 63, "www": [84, 97, 111], "x": [23, 24, 30, 34, 41, 42, 43, 56, 65, 83, 89, 93, 96, 102, 103], "x86": 85, "x86_64": 89, "xfm": 86, "xp": 92, "xu": [83, 88, 96, 107, 109], "y": [87, 89], "yac": [26, 31, 36, 39, 41, 42, 46, 49, 51, 53, 57, 64, 65, 66], "yaml": [46, 49, 51, 103, 106, 107], "yet": [85, 87, 89, 90, 100], "yield": [46, 47, 50, 102, 103, 111], "yml": 89, "you": [30, 56, 83, 85, 86, 87, 88, 89, 90, 92, 93, 94, 96, 97, 98, 99, 100, 102, 103, 104, 107, 109, 110], "your": [85, 86, 87, 88, 89, 92, 94, 95, 96, 97, 99, 103, 109, 110], "yourself": [89, 94], "yymmdd": 100, "z": 100, "zenodo": [104, 107], "zero": [14, 20, 32, 33, 47, 48, 56, 73, 78], "zeropad2d": 32, "zeropad2dtest": 32, "zmax": 34, "zmin": 34, "zoom": [38, 39, 46, 63, 64, 66], "zoom2d": [40, 65], "zoom3d": 40, "zuckerberg": [83, 96]}, "titles": ["CerebNet", "CerebNet.dataloader", "CerebNet.datasets", "CerebNet_models", "CerebNet.utils", "FastSurferCNN", "FastSurferCNN.data_loader", "FastSurferCNN.models", "FastSurferCNN.utils", "HypVINN", "HypVINN.data_loader", "HypVINN.models", "HypVINN.utils", "CerebNet.apply_warp", "CerebNet.data_loader.augmentation", "CerebNet.data_loader.data_utils", "CerebNet.data_loader.dataset", "CerebNet.data_loader.loader", "CerebNet.datasets.generate_hdf5", "CerebNet.datasets.load_data", "CerebNet.datasets.utils", "CerebNet.datasets.wm_merge_clean", "CerebNet.inference", "CerebNet.models.networks", "CerebNet.models.sub_module", "CerebNet.run_prediction", "CerebNet.utils.checkpoint", "CerebNet.utils.load_config", "CerebNet.utils.lr_scheduler", "CerebNet.utils.meters", "CerebNet.utils.metrics", "CerebNet.utils.misc", "FastSurferCNN.data_loader.augmentation", "FastSurferCNN.data_loader.conform", "FastSurferCNN.data_loader.data_utils", "FastSurferCNN.data_loader.dataset", "FastSurferCNN.data_loader.loader", "FastSurferCNN.download_checkpoints", "FastSurferCNN.generate_hdf5", "FastSurferCNN.inference", "FastSurferCNN.models.interpolation_layer", "FastSurferCNN.models.losses", "FastSurferCNN.models.networks", "FastSurferCNN.models.sub_module", "FastSurferCNN.quick_qc", "FastSurferCNN.reduce_to_aseg", "FastSurferCNN.run_prediction", "FastSurferCNN.segstats", "FastSurferCNN.utils.arg_types", "FastSurferCNN.utils.checkpoint", "FastSurferCNN.utils.common", "FastSurferCNN.utils.load_config", "FastSurferCNN.utils.logging", "FastSurferCNN.utils.lr_scheduler", "FastSurferCNN.utils.mapper", "FastSurferCNN.utils.meters", "FastSurferCNN.utils.metrics", "FastSurferCNN.utils.misc", "FastSurferCNN.utils.parser_defaults", "FastSurferCNN.utils.run_tools", "FastSurferCNN.utils.threads", "FastSurferCNN.version", "HypVINN.data_loader.data_utils", "HypVINN.data_loader.dataset", "HypVINN.inference", "HypVINN.models.networks", "HypVINN.run_prediction", "recon_surf.N4_bias_correct", "recon_surf.align_points", "recon_surf.align_seg", "recon_surf.create_annotation", "recon_surf.fs_balabels", "recon_surf.lta", "recon_surf.map_surf_label", "recon_surf.paint_cc_into_pred", "recon_surf.rewrite_mc_surface", "recon_surf.rewrite_oriented_surface", "recon_surf.rotate_sphere", "recon_surf.sample_parc", "recon_surf.smooth_aparc", "recon_surf.spherically_project_wrapper", "FastSurfer API", "recon_surf", "Welcome to FastSurfer!", "Contributor Covenant Code of Conduct", "Contributing to FastSurfer", "Manual Edits", "Examples", "FastSurfer Flags", "Installation", "Longitudinal Processing", "Output files", "Quick Start", "Security Policy", "Docker Support", "User Guide", "Introduction to FastSurfer", "FastSurfer License", "Singularity Support", "BATCH: brun_fastsurfer.sh", "SLURM: srun_fastsurfer.sh", "Advanced scripts", "CerebNet: run_prediction.py", "FastSurferCNN: run_prediction.py", "FastSurferCNN: download_checkpoints.py", "FastSurferCNN: generate_hdf5.py", "FastSurferCNN: run_model.py", "HypVINN: run_prediction.py", "Scripts", "LONG: long_fastsurfer.sh", "Surface pipeline: recon-surf.sh", "FastSurferCNN: segstats.py", "FastSurfer Utilities"], "titleterms": {"04": 89, "1": [87, 89, 92, 94, 110], "2": [87, 89, 92, 94, 110], "20": 89, "22": 89, "3": [87, 89, 94, 110], "4": [87, 89, 110], "5": [87, 89], "6": 87, "NOT": 86, "acceler": 89, "acknowledg": [83, 96], "advanc": [94, 101, 102, 107, 111], "ai": 89, "align_point": 68, "align_seg": 69, "also": 46, "amd": [89, 94], "an": 85, "apach": 97, "api": 81, "appl": 89, "apply_warp": 13, "ar": 86, "arg_typ": 48, "argument": [88, 102, 103, 104, 105, 106, 107, 111], "asegdkt_segfil": 86, "attest": 94, "attribut": [84, 85], "augment": [14, 32], "batch": 99, "befor": 85, "behind": 90, "best": [94, 98], "bia": 86, "brun_fastsurf": 99, "bug": 85, "build": [94, 98], "buildkit": 94, "can": 86, "cerebnet": [0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 91, 102], "cerebnet_model": 3, "cfg": 107, "checkpoint": [26, 49, 103, 107], "citat": 107, "click": 92, "cluster": 87, "code": [84, 85], "colab": 92, "command": [103, 106, 111], "commandlin": [103, 104, 105, 106, 111], "common": 50, "complet": 92, "conda": 89, "conduct": 84, "config": 103, "conform": 33, "contribut": 85, "contributor": 84, "correct": 86, "coven": 84, "cpu": [89, 94], "create_annot": 70, "creation": 94, "current": 89, "data": [90, 106], "data_load": [6, 10, 14, 15, 16, 17, 32, 33, 34, 35, 36, 62, 63], "data_util": [15, 34, 62], "dataload": 1, "dataset": [2, 16, 18, 19, 20, 21, 35, 63], "debug": 100, "default": [99, 106, 107], "depend": 89, "develop": 107, "directori": 103, "do": [85, 86], "docker": [87, 88, 89, 92, 94, 110], "dockerhub": 94, "document": 107, "download_checkpoint": [37, 104], "downstream": 96, "dual": 99, "easi": 92, "edit": 86, "effect": 86, "enforc": 84, "enhanc": 85, "environ": 89, "evalu": 103, "exampl": [87, 94, 103, 106, 110], "experienc": 86, "experiment": [89, 94], "expert": 96, "fastsurf": [81, 83, 85, 87, 88, 89, 92, 94, 96, 97, 98, 107, 112], "fastsurfercnn": [5, 6, 7, 8, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 103, 104, 105, 106, 111], "fastsurfervinn": 106, "field": 86, "file": [91, 107], "final": 90, "flag": [87, 88, 94, 98, 110], "freesurf": [86, 89, 96], "from": 94, "fs_balabel": 71, "full": [88, 103, 104, 105, 106, 111], "gener": [86, 94, 103], "generate_hdf5": [18, 38, 105], "good": 85, "googl": 92, "gpu": [89, 94, 98], "guid": [86, 95], "h": 111, "help": 109, "hemi": 87, "home": 98, "how": [85, 90], "hypvinn": [9, 10, 11, 12, 62, 63, 64, 65, 66, 91, 107], "i": [85, 90], "imag": [94, 98, 107], "infer": [22, 39, 64], "input": 107, "insid": 110, "instal": [89, 110], "intel": 89, "intend": 96, "interfac": [103, 104, 105, 106, 111], "interpolation_lay": 40, "introduct": 96, "licens": 97, "linux": 89, "list": [88, 99], "load": 107, "load_config": [27, 51], "load_data": 19, "loader": [17, 36], "log": 52, "long": 109, "long_fastsurf": 109, "longitudin": 90, "loss": 41, "lr_schedul": [28, 53], "lta": 72, "maco": 89, "manual": 86, "map_surf_label": 73, "mapper": 54, "matter": 86, "measur": 111, "meter": [29, 55], "metric": [30, 56], "minimum": 96, "misc": [31, 57, 106], "model": [7, 11, 23, 24, 40, 41, 42, 43, 65, 106, 107], "modul": [83, 88, 91, 96, 110], "mount": 98, "multipl": [87, 110], "n4_bias_correct": 67, "name": [102, 103, 104, 105, 106, 107, 111], "nativ": [87, 89, 110], "network": [23, 42, 65, 107], "notebook": 92, "offici": [94, 98], "onli": 89, "optim": 106, "option": [88, 102, 103, 106, 107, 111], "other": 88, "our": 84, "output": [91, 107], "overview": [83, 86, 110], "own": 98, "packag": 89, "paint_cc_into_pr": 74, "parallel": [87, 99], "paramet": 107, "parser_default": 58, "pial": 86, "pipelin": [86, 88, 99, 107, 110], "placement": 86, "pledg": 84, "polici": 93, "posit": [102, 104, 106], "possibl": 86, "practic": [94, 98], "process": [86, 87, 90, 99, 107], "proven": 94, "pull": 94, "py": [102, 103, 104, 105, 106, 107, 111], "python": 89, "question": 99, "quick": [87, 92], "quick_qc": 44, "recon": 110, "recon_surf": [67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 82], "reconstruct": 83, "reduce_to_aseg": 45, "refer": [83, 90, 96], "registr": 86, "report": [85, 93], "requir": [88, 89, 96, 107], "resolut": 106, "respons": 84, "rewrite_mc_surfac": 75, "rewrite_oriented_surfac": 76, "rotate_spher": 77, "run": [87, 88, 90, 94, 100, 107], "run_model": 106, "run_predict": [25, 46, 66, 102, 103, 107], "run_tool": 59, "sample_parc": 78, "scene": 90, "scope": 84, "script": [101, 108], "secur": 93, "see": [46, 107], "segment": [83, 86, 87, 88, 91, 92], "segstat": [47, 111], "serial": 99, "set": 94, "sh": [99, 100, 109, 110], "shown": 111, "side": 86, "singl": [99, 103, 106, 110], "singular": [87, 89, 92, 98, 110], "slurm": [87, 100], "smooth_aparc": 79, "some": 88, "spherically_project_wrapp": 80, "srun_fastsurf": 100, "standard": 84, "start": 92, "statist": 90, "step": 107, "sub": 111, "sub_modul": [24, 43], "subject": [87, 99, 103, 110], "subjectx": [87, 110], "submit": 85, "subopt": 111, "suggest": 85, "support": [89, 93, 94, 98], "surf": 110, "surfac": [83, 86, 88, 91, 110], "system": [89, 96], "talairach": 86, "technic": 107, "text": 109, "thread": 60, "three": 92, "tool": 107, "train": 106, "tutori": 92, "ubuntu": 89, "us": [86, 96], "usag": [96, 98, 99, 100, 107, 109, 110], "user": [86, 95], "util": [4, 8, 12, 20, 26, 27, 28, 29, 30, 31, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 112], "version": [61, 89, 93], "via": 87, "vulner": 93, "weight": 107, "welcom": 83, "what": [86, 90], "when": [86, 88], "white": 86, "whole": 103, "window": 89, "without": 98, "wm_merge_clean": 21, "your": [90, 98]}}) \ No newline at end of file