Deep-MI/FastSurfer v2.5.0 on GitHub

Main Updates

Integration of the new and very much improved Corpus Callosum Segmentation, including CC thickness, curvature analysis, see https://deep-mi.org/FastSurfer/dev/overview/modules/CC.html and our paper, published in Imaging Neuroscience https://doi.org/10.1162/IMAG.a.1221 , pdf also here: https://arxiv.org/abs/2511.16471
Native Image: Experimental, with the --keepgeom or --native_image flag we now allow to perform the segmentation (--seg_only !!) in the native image space. For this the image should be close to isotropic voxel sizes.
Our Lesion Inpainting Tool neuroLIT is now experimentally integrated into FastSurfer to permit processing images with a lesion mask or resection and generating surface models etc. https://doi.org/10.1162/imag_a_00446 https://deep-mi.org/FastSurfer/dev/overview/modules/LIT.html
Improved eTIV stability. Still based on the FreeSurfer-like registration approach, but with a more stable pre-alignment to avoid mis-registrations and incorrect eTIV values, e.g. in HCP data. Addressing, e.g. #800 . Also watch out for our own superior segmentation based eTIV tools in future releases.
Added a MacOS build packaging
Various minor fixes and improvement (see below).

What's Changed

Update LONG.md by @m-reuter in #665
Prevent division by zero by @santiestrada32 in #667
Fix smaller issues in srun_fastsurfer.sh by @dkuegler in #671
Fix regmode none for hypvinn by @dkuegler in #675
Move existing surfaces check into run_fastsurfer by @dkuegler in #677
Mac compatibility: Avoid PCRE grep in recon-surf, stat formatting and mapfile by @dkuegler in #672
Read the voxel size from image with python instead of from log by @dkuegler in #683
quicktest update & merge CerebNet.utils.metrics into FastSurferCNN.utils.metrics by @taha-abdullah in #590
Update doc for Docker in the rootless mode by @plu-project in #684
Add additional stats/aseg.VINN.stats file by @dkuegler in #678
Update matplotlib by @santiestrada32 in #687
Fix links to actions in quicktest workflow by @dkuegler in #686
Add documentation to build the docker image releases by @dkuegler in #689
Fix how devices were parsed in brun_fastsurfer by @dkuegler in #690
Add segmentation of images in "native image space" by @dkuegler in #691
Some formatting changes that have accumulated over time by @dkuegler in #692
Fixes to the anisotropic segmentation of FastSurfer by @dkuegler in #695
Bump setuptools from 75.8.0 to 78.1.1 by @dependabot[bot] in #696
Fixes so de-selecting views for processing for run_prediction is possible by @dkuegler in #697
Data documentation by @kdiers in #419
Bump tornado from 6.4.2 to 6.5.1 by @dependabot[bot] in #698
Add information about FastSurfer course by @kdiers in #711
Fix conform.py losing tr value during conversion by @OtabekRintaro in #714
Fix ruff error suppression of typing.Optional by @OtabekRintaro in #713
Fix import in brun_fastsurfer by @dkuegler in #715
Bump urllib3 from 2.3.0 to 2.5.0 by @dependabot[bot] in #710
Bump requests from 2.32.3 to 2.32.4 by @dependabot[bot] in #706
Bump protobuf from 5.28.3 to 5.29.5 by @dependabot[bot] in #707
Bump torch from 2.6.0+cpu to 2.7.1+cpu by @dependabot[bot] in #708
Add workaround for SSL certificate mismatch error with mamba/conda at DZNE by @dkuegler in #718
Bugfixes before release by @dkuegler in #700
Fix inconsistent file and folder permissions by @dkuegler in #719
Github workflow changes by @dkuegler in #720
Add Docker command and revise longitudinal notes by @m-reuter in #725
Change "base" to person-specific template by @m-reuter in #726
Fix typos in LONG.md by @christianewert in #729
Add the longitudinal outputs compatibility script by @dkuegler in #722
Avoid ' without termination in help text by @m-reuter in #731
Fix ROCm installation link for AMD GPU support by @cbrnr in #735
Fix srun_fastsurfer termination on files inspection by @dkuegler in #741
Fix quicktest outputs if FastSurfer fails by @dkuegler in #742
Fix and update spherical project by @dkuegler in #743
Add MacOS build packaging tool by @OtabekRintaro in #734
Fix subshells exiting not leading to script ending by @dkuegler in #749
Updates in preparation for FastSurferCC by @dkuegler in #750
Minor fixes to the documentation, formatting and literal strings. by @dkuegler in #751
Add a template pre-commit hook script and speed up sphinx build by @dkuegler in #755
Maintenance update for FastSurfer (coming from FastSurferCC integration) by @dkuegler in #757
Documentation better linking of symbols to files and cleanup by @dkuegler in #760
Add FastSurfer-CC to the FastSurfer repository by @ClePol in #727
FastSurfer-CC bugfixes by @ClePol in #762
CC documentation & final testing by @ClePol in #763
Quick fix to address warning in run_prediction.py by @dkuegler in #768
Change error message to warning in link_fs.sh by @m-reuter in #771
Exclude WarmupCosineLR.step from doc validation by @m-reuter in #772
Various updates and changes to the documentation by @dkuegler in #765
Add citation for FastSurfer-CC by @ClePol in #773
Add timeout to version.py execution by @m-reuter in #774
bump python packages, use UV instead of conda, update docker build by @dkuegler in #766
Fix version info by @dkuegler in #776
Internal benchmarking/execution time for segmentation pipeline by @dkuegler in #777
Modify the macOS release script to remove the link_fs.sh duplicate file by @dkuegler in #775
Fixes to the docker build process by @dkuegler in #781
Quickfix: Fix typo in functions.sh by @dkuegler in #783
Fix voxel radius calculation in sample_parc.py by @m-reuter in #784
add stages to long_fastsurfer.sh by @m-reuter in #786
Change and harmonize 0 or 1 as boolean values to "true"/"false" in bash scripts by @dkuegler in #785
Remove corpus callosum processing from surface pipeline by @dkuegler in #787
Fix bug in spherically project wrapper by @dkuegler in #788
Add missing files to the documentation by @dkuegler in #792
CC module bugfix and robustness by @ClePol in #791
Add missing '[@]' to function RunBatchJobs by @dkuegler in #793
Fix: Correct FastSurfer-CC error code handling and documentation formatting by @dkuegler in #794
Update pre-commit script and GitHub workflows to use uv by @dkuegler in #796
Fix the matplotlib backend for qc plotting by @dkuegler in #797
Upgrade WhipperSnapPy from 1.3 to 2.1, simplify and streamline integration by @ClePol in #795
Fix: symlink may point to absolute path by @dkuegler in #799
CC midplane refinement by @ClePol in #801
Minor maintenance fixes to FastSurfer by @dkuegler in #804
Fix image reorientation and cropping bugs in conform workflow (fixes #764) by @dkuegler in #767
Minor bugfixes and docfixes by @ClePol in #805
replace requirements.mac.txt with pyproject.toml by @m-reuter in #808
Lesion inpainting (LIT) integration by @ClePol in #803
Fix usage of Reorientation logic in CerebNet and HypVINN by @dkuegler in #809
Improve talairach transform and etiv estimation through atlas prealignment by @kdiers in #807
Fix aniso by @m-reuter in #810
CC surface alignment + subsegment ordering by @ClePol in #812
Replace local LTA, alignment, and point-registration code with neuroreg by @m-reuter in #811
fix doc strings for conforming by @m-reuter in #813
CC documentation update by @ClePol in #814
Fix strict conform voxel center to agree with FreeSurfer and earlier FastSurfer versions by @m-reuter in #815
Release docker changes by @ClePol in #816

New Contributors

@plu-project made their first contribution in #684
@OtabekRintaro made their first contribution in #714
@christianewert made their first contribution in #729
@cbrnr made their first contribution in #735

Full Changelog: v2.4.2...v2.5.0

Deep-MI/FastSurfer v2.5.0 FastSurfer v2.5.0 on GitHub

Main Updates

What's Changed

New Contributors

Deep-MI/FastSurfer v2.5.0
FastSurfer v2.5.0

on GitHub