The hipsta scripts can also be run within a Python environment:
-import hipsta
+import hipsta
hipsta.run_hipsta(filename="my_filename.mgz", hemi="lh", lut="freesurfer", outputdir="my_output_directory")
A full list of available arguments for the run_hipsta function can be obtained with:
-import hipsta
+import hipsta
help(hipsta.run_hipsta)
@@ -582,7 +582,7 @@ References:
- Copyright © 2024, Kersten Diers
+ Copyright © 2025, Kersten Diers
Made with
Furo
@@ -638,7 +638,7 @@ References:
-
+
diff --git a/dev/genindex.html b/dev/genindex.html
index 060783f..9b53535 100644
--- a/dev/genindex.html
+++ b/dev/genindex.html
@@ -4,8 +4,8 @@
- Index - Hipsta
-
+ Index - Hipsta
+
@@ -278,7 +278,7 @@ R
- Copyright © 2024, Kersten Diers
+ Copyright © 2025, Kersten Diers
Made with
Furo
@@ -305,7 +305,7 @@ R
-
+
diff --git a/dev/index.html b/dev/index.html
index b1331c9..1d96da5 100644
--- a/dev/index.html
+++ b/dev/index.html
@@ -5,9 +5,9 @@
-
+
Hipsta
-
+
@@ -308,7 +308,7 @@ License¶
-
+
diff --git a/dev/search.html b/dev/search.html
index d64123c..d768934 100644
--- a/dev/search.html
+++ b/dev/search.html
@@ -5,9 +5,9 @@
-
+
-Search - Hipsta
+Search - Hipsta
@@ -266,7 +266,7 @@
- Copyright © 2024, Kersten Diers
+ Copyright © 2025, Kersten Diers
Made with
Furo
@@ -293,7 +293,7 @@
-
+
diff --git a/dev/searchindex.js b/dev/searchindex.js
index 2516943..df15317 100644
--- a/dev/searchindex.js
+++ b/dev/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"alltitles": {"1. Image processing": [[6, "image-processing"]], "10. Mapping of subfield labels (and other volume-based data, optional)": [[6, "mapping-of-subfield-labels-and-other-volume-based-data-optional"]], "11. Creation supplementary files for visualization": [[6, "creation-supplementary-files-for-visualization"]], "2. Label processing": [[6, "label-processing"]], "3. Mask processing": [[6, "mask-processing"]], "4. Surface creation": [[6, "surface-creation"]], "5. Creation of a tetrahedral mesh": [[6, "creation-of-a-tetrahedral-mesh"]], "6. Creation of label files for the tetra mesh": [[6, "creation-of-label-files-for-the-tetra-mesh"]], "7. Cutting of the tetra mesh at anterior and posterior ends": [[6, "cutting-of-the-tetra-mesh-at-anterior-and-posterior-ends"]], "8. Cube parametrization": [[6, "cube-parametrization"]], "9. Thickness and curvature computation": [[6, "thickness-and-curvature-computation"]], "API Reference": [[2, null]], "Additional arguments for ASHS and FreeSurfer segmentations": [[6, "additional-arguments-for-ashs-and-freesurfer-segmentations"]], "Additional arguments for ASHS segmentations": [[6, "additional-arguments-for-ashs-segmentations"]], "As a command-line script:": [[4, "as-a-command-line-script"]], "As a python package:": [[4, "as-a-python-package"]], "Automated QC": [[6, "automated-qc"]], "Changes": [[3, null]], "Common issues": [[6, "common-issues"]], "Cutting issues": [[6, "cutting-issues"]], "Description:": [[4, "description"]], "Documentation": [[4, null]], "Evaluating the output": [[6, "evaluating-the-output"]], "Hipsta": [[5, null]], "Holes in the surface": [[6, "holes-in-the-surface"]], "Input images": [[6, "input-images"]], "Installation": [[5, "installation"]], "License": [[5, "license"]], "Logfiles": [[6, "logfiles"]], "Mandatory arguments": [[6, "mandatory-arguments"]], "Manual QC": [[6, "manual-qc"]], "Outputs:": [[4, "outputs"]], "Processing steps": [[6, "processing-steps"]], "Purpose:": [[4, "purpose"]], "QC": [[6, "qc"]], "References:": [[4, "references"]], "Requirements:": [[4, "requirements"]], "Running an analysis": [[6, "running-an-analysis"]], "Supported segmentations:": [[4, "supported-segmentations"]], "Troubleshooting": [[6, "troubleshooting"]], "Tutorial": [[6, null]], "Usage:": [[4, "usage"]], "hipsta.run_hipsta": [[0, null]], "hipsta.utils.map_values.mapValues": [[1, null]], "v0.1.0-beta": [[3, "v0-1-0-beta"]], "v0.1.1-beta": [[3, "v0-1-1-beta"]], "v0.2.0-beta": [[3, "v0-2-0-beta"]], "v0.3.0-beta": [[3, "v0-3-0-beta"]], "v0.4.0-beta": [[3, "v0-4-0-beta"]], "v0.8.0-beta": [[3, "v0-8-0-beta"]]}, "docnames": ["api/generated/hipsta.run_hipsta", "api/generated/hipsta.utils.map_values.mapValues", "api/index", "changes/index", "documentation/index", "index", "tutorials/index"], "envversion": {"nbsphinx": 4, "sphinx": 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index 282219f..86add7e 100644
--- a/dev/tutorials/index.html
+++ b/dev/tutorials/index.html
@@ -5,9 +5,9 @@
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+
Tutorial - Hipsta
-
+
@@ -685,7 +685,7 @@ Cutting issues