Fix aniso

[m-reuter]

Fixes:

• write invocation of run_fastsurfer to log files (was overwritten by version.py, now writes into the seg and build logs)
• bug where segmentations were cropped when using keepgeom in special cases.
• CC can now draw its result back into aparc+aseg.dkt if both images are native geometry
• CC now can also fill WM and background voxels for those cases (due to internal re-orientation to soft LIA in a new wrapper)

[Copilot]

Pull request overview

This PR addresses two pipeline robustness issues: (1) preserving run_fastsurfer.sh invocation details in log files without being overwritten by version.py, and (2) preventing unintended cropping/shift during “soft” reorientation/keep-geometry workflows (notably affecting anisotropic/native-geometry segmentations).

Changes:

• Log the fully shell-escaped run_fastsurfer.sh invocation into the segmentation log and append it to the build log generated by version.py.
• Fix/guard “soft” target-orientation reorientation to fall back to a discrete flip/reorder (no interpolation) when appropriate, plus add regression tests for non-cubic and keepgeom-like cases.
• Add --keepgeom/--native_image support to paint_cc_into_pred.py and route CC post-processing through a temporary LIA space when needed.

Reviewed changes

Copilot reviewed 10 out of 11 changed files in this pull request and generated 7 comments.

Show a summary per file

File	Description
test/image/test_orientation_transform.py	Adds regression tests ensuring soft reorientation roundtrips exactly without cropping for non-cubic/keepgeom-like inputs.
run_fastsurfer.sh	Records a properly quoted invocation string in logs; passes --keepgeom through to CC inpainting when native geometry is requested.
FastSurferCNN/version.py	Small refactor in read_and_close_version type handling (currently introduces a runtime issue).
FastSurferCNN/data_loader/conform.py	Improves soft reorientation path to prefer discrete transforms when no interpolation is required; minor formatting/type-check refactors (currently introduces runtime issues).
CorpusCallosum/utils/visualization.py	Refactors isinstance check (currently introduces a runtime issue).
CorpusCallosum/shape/mesh.py	Refactors isinstance check (currently introduces a runtime issue).
CorpusCallosum/registration/midsagittal_plane_alignment.py	Minor refactor (list-comp to generator unpacking).
CorpusCallosum/paint_cc_into_pred.py	Adds --keepgeom CLI flag; allows non-LIA inputs in keepgeom mode and performs correction in temporary LIA orientation with mapping back.
CorpusCallosum/fastsurfer_cc.py	Minor refactor (list-comp to generator unpacking).
CorpusCallosum/data/read_write.py	Refactors isinstance check (currently introduces a runtime issue).
.gitignore	Ignores /checkpoints/**.

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