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Pull request overview
This PR consolidates a set of maintenance updates across the FastSurfer codebase, spanning Docker build tooling, shell entrypoints, docs, and a broad set of Python typing/logging cleanups.
Changes:
- Refactors FreeSurfer license auto-detection into a reusable shell helper and wires it into
run_fastsurfer.shand SLURM tooling. - Improves Docker build metadata/tagging and adjusts locale handling in the Docker image.
- Performs widespread typing/logging/formatting cleanups across FastSurferCNN, HypVINN, CerebNet, and CorpusCallosum modules.
Reviewed changes
Copilot reviewed 24 out of 25 changed files in this pull request and generated 16 comments.
Show a summary per file
| File | Description |
|---|---|
| tools/Docker/build.py | Updates dry-run printing, adds repository URL detection, tweaks image tag/build args. |
| tools/Docker/Dockerfile | Adjusts locale generation/install and environment variables. |
| stools.sh | Reuses recon-surf helper to auto-detect FreeSurfer license for SLURM scripts. |
| run_fastsurfer.sh | Replaces inline FS license checks with auto_detect_fs_license. |
| recon_surf/recon-surf.sh | Minor user-facing error message reflow. |
| recon_surf/functions.sh | Adds auto_detect_fs_license helper and tweaks command logging/spelling. |
| pyproject.toml | Adds ty to the style extra. |
| doc/overview/SINGULARITY.md | Adds a new “Common problems” warning explanation and adjusts formatting. |
| HypVINN/utils/img_processing_utils.py | Updates typing and orientation logging via aff2axcodes. |
| HypVINN/data_loader/data_utils.py | Tightens dtype/shape typing and minor array casting changes. |
| FastSurferCNN/version.py | Typing-oriented refactors and build-file parsing tweaks. |
| FastSurferCNN/utils/common.py | Path/typing tweaks and docstring formatting changes. |
| FastSurferCNN/utils/brainvolstats.py | Typing hardening, input validation for masking helpers, and internal refactors. |
| FastSurferCNN/utils/init.py | Reworks exported typing aliases and adds check_literal_type. |
| FastSurferCNN/segstats.py | Switches user output from print to logger. |
| FastSurferCNN/run_prediction.py | Typing cleanups and small refactors in config handling and tensor initialization. |
| FastSurferCNN/quick_qc.py | Migrates CLI parsing to argparse and replaces prints with structured logging. |
| FastSurferCNN/data_loader/data_utils.py | Adds stronger typing, minor safety checks, and LUT parsing refactor. |
| CorpusCallosum/utils/visualization.py | Replaces removed noop context with nullcontext for backend switching. |
| CorpusCallosum/utils/mapping_helpers.py | Updates matrix typing alias usage for nodding correction. |
| CorpusCallosum/paint_cc_into_pred.py | Removes leftover debug prints. |
| CorpusCallosum/data/read_write.py | Updates header typing alias for Mdc matrix. |
| CerebNet/data_loader/dataset.py | Typing additions/refactors and sample dict construction changes. |
| .gitignore | Ignores /tools/debug-helpers. |
| .dockerignore | Refines docker build context ignores (venv, docs, tooling, lockfiles, etc.). |
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…bugfix to the property SubjectDirectory.asegdkt_segfile
Use this function in srun_fastsurfer and run_fastsurfer.sh
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- make quick_qc.py follow the general formatting style - add ty into style extra (pyproject.toml) - Make brainvolstats satisfy ty typing rules
Add en_US.UTF-8 and C.UTF-8 to fix locale warnings. Update Singularity doc (workdir warning). Fix sep=>end argument in build.py's print statements on --print. Fix the default tag of the docker image, if no tag name is given (added v) and the --tag_dev default (<DEVICE>-dev instead of dev<DEVICE>-)
Formatting Cleanup
Fix formatting
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Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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srun_fastsurfer.sh.Overall, this PR does not add a feature, but brings together smaller fixes and cleanups that have piled up over time.