ENH: Add reporting workflow for BOLD fit #3082
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Codecov ReportPatch coverage:
Additional details and impacted files@@ Coverage Diff @@
## next #3082 +/- ##
==========================================
- Coverage 47.41% 47.09% -0.32%
==========================================
Files 49 49
Lines 3984 4015 +31
==========================================
+ Hits 1889 1891 +2
- Misses 2095 2124 +29
☔ View full report in Codecov by Sentry. |
|
Example reports: Generally we've used blue contours to indicate white matter boundaries, so I'll update that. I would also like to create a 3-way image that shows the boldref, the fieldmap reference mapped onto the boldref, and the fieldmap (in Hz) overlaid on the boldref. @oesteban Any thoughts on how to make that last happen? |
Flickering through three frames is not possible ATM. We would need to refactor the JS code we embed in the SVGs. However, if you don't mind the fieldmap overlay to be fixed in both (boldref and fmapref), then that should not be very difficult. And that plot makes a lot of sense to me. WDYT? |
|
Yeah, that sounds reasonable. |
|
This is basically ready for review. Edited top post with latest reports from CI. Going to make some small changes to the captions, but nothing that should postpone a review if anybody's available. |
|
Updated the reports in the first post. This is done. |
mgxd
reviewed
Sep 5, 2023
| summary.inputs.dummy_scans = config.workflow.dummy_scans | ||
|
|
||
| func_fit_reports_wf = init_func_fit_reports_wf( | ||
| # TODO: Enable sdc report even if we find coregref |
There was a problem hiding this comment.
Just to state this more clearly: I consider good report generation in the presence of pre-existing derivatives a second-class concern at the moment. I am okay putting out a release where that is incomplete or even containing known bugs, if that can get us to a stable state for future development and end the fork.
Made a copy of |
effigies
added a commit
that referenced
this pull request
Jan 10, 2024
23.2.0 (January 10, 2024) New feature release in the 23.2.x series. This release wraps up a significant refactor of fMRIPrep. The main new features can be used with the ``--level`` and ``--derivatives`` flags. The ``--level`` flag can take the arguments ``minimal``, ``resampling`` or ``full``. The default is ``full``, which should produce nearly the same results as previous versions. ``minimal`` will produce only the minimum necessary to deterministically generate the remaining derivatives. ``resampling`` will produce some additional derivatives, intended to simplify resampling with other tools. The ``--derivatives`` flag takes arguments of the form ``name=/path/to/dir``, for example ``--derivatives anat=$SMRIPREP_DIR``. If provided, fMRIPrep will read the specified directories for pre-computed derivatives. If a derivative is found, it will be used instead of computing it from scratch. If a derivative is not found, fMRIPrep will compute it and proceed as usual. Taken together, these features can allow a dataset provider to run a minimal fMRIPrep run, targeting many output spaces, while a user can then run a ``--derivatives`` run to generate additional derivatives in only the output spaces they need. Another use case is to provide an precomputed derivative to override the default fMRIPrep behavior, enabling easier workarounds for bugs or experimentation with alternatives. Additionally, this release includes a number of bug fixes and improvements. This release adds support for MSM-Sulc, improving the alignment of subject surfaces to the fsLR template. This process is enabled by default, but may be disabled with the ``--no-msm`` flag. This release resolves a number of issues with fieldmaps inducing distortions during correction. Phase difference and direct fieldmaps are now masked correctly, preventing the overestimation of distortions outside the brain. Additionally, we now implement Jacobian weighting during unwarping, which corrects for compression and expansion effects on signal intensity. To disable Jacobian weighting, use ``--ignore fmap-jacobian``. Finally, a new resampling method has been added, to better account for susceptibility distortion and motion in a single shot resampling to a volumetric target space. We anticipate extending this to surface targets in the future. * FIX: Restore --ignore sbref functionality (#3180) * FIX: Retrieve atlas ROIs at requested density (#3179) * FIX: Keep minctracc executable in FreeSurfer installation (#3175) * FIX: Exclude echo entity from optimally combined derivatives (#3166) * FIX: Disable boldref-space outputs unless requested (#3159) * FIX: Tag memory estimates in resamplers (#3150) * FIX: Final revisions for next branch (#3134) * FIX: Minor fixes to work with MSMSulc-enabled smriprep-next (#3098) * FIX: Connect EPI-to-fieldmap transform (#3099) * FIX: Use Py2-compatible version file template for fmriprep-docker (#3101) * FIX: Update connections to unwarp_wf, convert ITK transforms to text (#3077) * ENH: Allow --ignore fmap-jacobian to disable Jacobian determinant modulation during fieldmap correction (#3186) * ENH: Exclude non-steady-state volumes from confound correlation plot (#3171) * ENH: Pass FLAIR images to anatomical workflow builder to include in boilerplate (#3146) * ENH: Restore carpetplot and other final adjustments (#3131) * ENH: Restore CIFTI-2 generation (#3129) * ENH: Restore resampling to surface GIFTIs (#3126) * ENH: Restore confound generation (#3120) * ENH: Restore resampling BOLD to volumetric templates (#3121) * ENH: Restore resampling to T1w target (#3116) * ENH: Add MSMSulc (#3085) * ENH: Add reporting workflow for BOLD fit (#3082) * ENH: Generate anatomical derivatives useful for resampling (#3081) * RF: Load reportlets interfaces from nireports rather than niworkflows (#3176, #3184) * RF: Separate goodvoxels mask creation from fsLR resampling (#3170) * RF: Write out anatomical template derivatives (#3136) * RF: Update primary bold workflow to incorporate single shot resampling (#3114) * RF: Update derivative cache spec, calculate per-BOLD, reuse boldref2fmap (#3078) * RF: Split fMRIPrep into fit and derivatives workflows (#2913) * RPT: Rename CSF/WM confounds in fMRIPlot (#3172) * TST: Add smoke tests for full workflow and most branching flags (#3155) * TST: Add smoke-tests for bold_fit_wf (#3152) * DOC: Fix documentation and description for init_bold_grayords_wf (#3051) * DOC: Minor updates in outputs.rst (#3148) * STY: Apply a couple refurb suggestions (#3151) * STY: Fix flake8 warnings (#3044) * STY: Apply pyupgrade suggestions (#3043) * MNT: Restore mritotal subcommands to Dockerfile (#3149) * MNT: Update smriprep to 0.13.1 (#3153) * MNT: optimise size of PNG files (#3145) * MNT: update vendored docs script ``github_link.py`` (#3144) * MNT: Update tedana pin, test on Python 3.12 (#3141) * MNT: Bump environment (#3132) * MNT: Bump version requirements (#3107) * MNT: http:// → https:// (#3097) * MNT: Remove mritotal and dependencies from FreeSurfer ignore file (#3090) * MNT: Update environment (#3073) * MNT: Depend on newer sphinx (#3067) * MNT: Install ANTs from conda-forge (#3061) * MNT: Drop Python 3.8 and numpy 1.21 support (NEP29) (#3052) * MNT: update update_zenodo.py script (#3042) * MNT: Fix welcome message formatting and instructions (#3039) * MNT: Python 3.11 should be supported (#3038) * CI: Bump actions/setup-python from 4 to 5 (#3181) * CI: Stop testing legacy layout (#3079) * CI: Improve tag detection for docker builds (#3066) * CI: Clean up pre-release builds (#3040)
NingAnMe
added a commit
to NingAnMe/fmriprep
that referenced
this pull request
Jan 11, 2024
23.2.0 (January 10, 2024) New feature release in the 23.2.x series. This release wraps up a significant refactor of fMRIPrep. The main new features can be used with the ``--level`` and ``--derivatives`` flags. The ``--level`` flag can take the arguments ``minimal``, ``resampling`` or ``full``. The default is ``full``, which should produce nearly the same results as previous versions. ``minimal`` will produce only the minimum necessary to deterministically generate the remaining derivatives. ``resampling`` will produce some additional derivatives, intended to simplify resampling with other tools. The ``--derivatives`` flag takes arguments of the form ``name=/path/to/dir``, for example ``--derivatives anat=$SMRIPREP_DIR``. If provided, fMRIPrep will read the specified directories for pre-computed derivatives. If a derivative is found, it will be used instead of computing it from scratch. If a derivative is not found, fMRIPrep will compute it and proceed as usual. Taken together, these features can allow a dataset provider to run a minimal fMRIPrep run, targeting many output spaces, while a user can then run a ``--derivatives`` run to generate additional derivatives in only the output spaces they need. Another use case is to provide an precomputed derivative to override the default fMRIPrep behavior, enabling easier workarounds for bugs or experimentation with alternatives. Additionally, this release includes a number of bug fixes and improvements. This release adds support for MSM-Sulc, improving the alignment of subject surfaces to the fsLR template. This process is enabled by default, but may be disabled with the ``--no-msm`` flag. This release resolves a number of issues with fieldmaps inducing distortions during correction. Phase difference and direct fieldmaps are now masked correctly, preventing the overestimation of distortions outside the brain. Additionally, we now implement Jacobian weighting during unwarping, which corrects for compression and expansion effects on signal intensity. To disable Jacobian weighting, use ``--ignore fmap-jacobian``. Finally, a new resampling method has been added, to better account for susceptibility distortion and motion in a single shot resampling to a volumetric target space. We anticipate extending this to surface targets in the future. * FIX: Restore --ignore sbref functionality (nipreps#3180) * FIX: Retrieve atlas ROIs at requested density (nipreps#3179) * FIX: Keep minctracc executable in FreeSurfer installation (nipreps#3175) * FIX: Exclude echo entity from optimally combined derivatives (nipreps#3166) * FIX: Disable boldref-space outputs unless requested (nipreps#3159) * FIX: Tag memory estimates in resamplers (nipreps#3150) * FIX: Final revisions for next branch (nipreps#3134) * FIX: Minor fixes to work with MSMSulc-enabled smriprep-next (nipreps#3098) * FIX: Connect EPI-to-fieldmap transform (nipreps#3099) * FIX: Use Py2-compatible version file template for fmriprep-docker (nipreps#3101) * FIX: Update connections to unwarp_wf, convert ITK transforms to text (nipreps#3077) * ENH: Allow --ignore fmap-jacobian to disable Jacobian determinant modulation during fieldmap correction (nipreps#3186) * ENH: Exclude non-steady-state volumes from confound correlation plot (nipreps#3171) * ENH: Pass FLAIR images to anatomical workflow builder to include in boilerplate (nipreps#3146) * ENH: Restore carpetplot and other final adjustments (nipreps#3131) * ENH: Restore CIFTI-2 generation (nipreps#3129) * ENH: Restore resampling to surface GIFTIs (nipreps#3126) * ENH: Restore confound generation (nipreps#3120) * ENH: Restore resampling BOLD to volumetric templates (nipreps#3121) * ENH: Restore resampling to T1w target (nipreps#3116) * ENH: Add MSMSulc (nipreps#3085) * ENH: Add reporting workflow for BOLD fit (nipreps#3082) * ENH: Generate anatomical derivatives useful for resampling (nipreps#3081) * RF: Load reportlets interfaces from nireports rather than niworkflows (nipreps#3176, nipreps#3184) * RF: Separate goodvoxels mask creation from fsLR resampling (nipreps#3170) * RF: Write out anatomical template derivatives (nipreps#3136) * RF: Update primary bold workflow to incorporate single shot resampling (nipreps#3114) * RF: Update derivative cache spec, calculate per-BOLD, reuse boldref2fmap (nipreps#3078) * RF: Split fMRIPrep into fit and derivatives workflows (nipreps#2913) * RPT: Rename CSF/WM confounds in fMRIPlot (nipreps#3172) * TST: Add smoke tests for full workflow and most branching flags (nipreps#3155) * TST: Add smoke-tests for bold_fit_wf (nipreps#3152) * DOC: Fix documentation and description for init_bold_grayords_wf (nipreps#3051) * DOC: Minor updates in outputs.rst (nipreps#3148) * STY: Apply a couple refurb suggestions (nipreps#3151) * STY: Fix flake8 warnings (nipreps#3044) * STY: Apply pyupgrade suggestions (nipreps#3043) * MNT: Restore mritotal subcommands to Dockerfile (nipreps#3149) * MNT: Update smriprep to 0.13.1 (nipreps#3153) * MNT: optimise size of PNG files (nipreps#3145) * MNT: update vendored docs script ``github_link.py`` (nipreps#3144) * MNT: Update tedana pin, test on Python 3.12 (nipreps#3141) * MNT: Bump environment (nipreps#3132) * MNT: Bump version requirements (nipreps#3107) * MNT: http:// → https:// (nipreps#3097) * MNT: Remove mritotal and dependencies from FreeSurfer ignore file (nipreps#3090) * MNT: Update environment (nipreps#3073) * MNT: Depend on newer sphinx (nipreps#3067) * MNT: Install ANTs from conda-forge (nipreps#3061) * MNT: Drop Python 3.8 and numpy 1.21 support (NEP29) (nipreps#3052) * MNT: update update_zenodo.py script (nipreps#3042) * MNT: Fix welcome message formatting and instructions (nipreps#3039) * MNT: Python 3.11 should be supported (nipreps#3038) * CI: Bump actions/setup-python from 4 to 5 (nipreps#3181) * CI: Stop testing legacy layout (nipreps#3079) * CI: Improve tag detection for docker builds (nipreps#3066) * CI: Clean up pre-release builds (nipreps#3040)
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Changes proposed in this pull request
TODO:
Results: