Add FastSurfer-CC to the FastSurfer repository#727

Merged

m-reuter merged 68 commits intoDeep-MI:devfrom

Jan 6, 2026

Commits on Jan 6, 2026

- Add extra typing with nibabelImage, VectorXd, ScalarType, etc. into several files
dkuegler
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added corpus callosum module

ClePol
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dkuegler
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updated requirements and removed mri_cc from recon-surf

ClePol
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dkuegler
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updated requirements, formatting, cleanup

ClePol
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dkuegler
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formatting and requirements fixes

ClePol
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dkuegler
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fix typo in comment

m-reuter
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dkuegler
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fixed spelling in comments

ClePol
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dkuegler
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added checkpoint donwloading

ClePol
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dkuegler
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added writing soft labels

ClePol
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dkuegler
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cc painting script for reconsurf integration

ClePol
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dkuegler
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added midslice based 3D subsegmentation in orig space outputs

ClePol
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dkuegler
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updated README and paths

ClePol
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dkuegler
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added partial volume corrected volume calculation, error messages and small bugfixes

ClePol
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sphinx doc build and license

ClePol
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dkuegler
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fix typos

m-reuter
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dkuegler
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added doc files for sphinx

ClePol
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dkuegler
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bugfixes for hires images, README updates, error handling

ClePol
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dkuegler
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improved contour extraction for thin CC and surface coordinates

ClePol
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dkuegler
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fixed freesurfer surface conversion and scaling issues

ClePol
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docstrings, typehints and small bugfixes

ClePol
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dkuegler
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cleaned up stats writing

ClePol
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dkuegler
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added consolidation strategy with WM and ventricle labels

ClePol
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dkuegler
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FastSurfer style weights loading + removed superflous plot

ClePol
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dkuegler
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recon-surf integration with FastSurferCNN label consolidation

ClePol
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dkuegler
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updated commandline interface

ClePol
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dkuegler
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Various documentation and formatting changes as well as optimizations during review
dkuegler
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Fixes broken by history rewrite (merge => rebase)
dkuegler
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Fixing problems introduced by incomplete changes in review
dkuegler
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rename files and standardize file names
dkuegler
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Fix doc build errors and ruff optimization codes
dkuegler
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updated helptexts & formatting

ClePol
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dkuegler
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documentation and review comments

ClePol
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dkuegler
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updated logging in paint_cc_into_pred and added missing docfiles

ClePol
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dkuegler
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Improve the left_right masking.
dkuegler
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Fix the CorpusCallosum documentation
dkuegler
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Remove --qc_output_dir and related functionality to simplify the fastsurfer_cc.py CLI interface and internal code complexity.
dkuegler
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file renaming, removed unused code, documentation update

ClePol
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dkuegler
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fixed commandline texts, parameter and absolute paths

ClePol
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dkuegler
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Rewrite of CCIndex, fixed middle slice selection argument, helptext

ClePol
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dkuegler
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Fix AC-PC localization
dkuegler
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Rework the generation of transformation matrices and make them more unified and clearer also fixing broken transformation matrices
dkuegler
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Fix docstrings and formatting in mesh.py
dkuegler
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Fix ruff errors
dkuegler
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updated helptext

ClePol
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dkuegler
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split cc_mesh class into cc_mesh and cc_contour

ClePol
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dkuegler
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updated cc visualization script with cleaner interface to Mesh, Contour, fsaverage. Fixed multithreading bug. Documentation

ClePol
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dkuegler
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cleaned up visualization script logic, removed unused CC contour code, multiple bugfixes

ClePol
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dkuegler
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Add the types file to merge all recurring types of FastSurferCC
dkuegler
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- Fix ruff and documentation errors
dkuegler
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Rename create_CC_mesh_from_contours to CCMesh.from_contours and make it a class method
dkuegler
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Fix surface output
dkuegler
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- Clean up docstrings, typing
dkuegler
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fixed label consolidation

ClePol
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dkuegler
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visualization & commandline interface bugfixes

ClePol
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- Fix saving the cc_surf (only saved when thickness_image was requested
dkuegler
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Fix and add explanation on how change cc_visualization.py
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Fix doc build error.
dkuegler
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Update CorpusCallosum to use the new lapy.Polygon interface.
dkuegler
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fixed for subsegmentation and lapy+cc contour

ClePol
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added advanced curvature metrics and refactored curvature calculation

ClePol
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bump lapy to 1.5.0 (instead of install from github)
dkuegler
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adressed fixmes, fixed bugs, added warnings

ClePol
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adressed review comments

ClePol
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dkuegler
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Fix the types of CCMeasuresDict.thickness_profile and ContourList
dkuegler
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Fix endpoint extraction and rotation of offsets (for endpoint extraction)
dkuegler
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Fix doc and style
dkuegler
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fixed stats (subseg-area, ordering, etc.), improved visualization

ClePol
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dkuegler
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fix 3d visualization
ClePol
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