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Pull request overview
This PR folds in small, targeted changes to improve determinism and runtime in the recon_surf “surf stream”, and makes a surface header sanity check more robust.
Changes:
- Make spectral spherical projection deterministic by seeding the eigen-solver RNG.
- Speed up
mode_filter()by avoiding per-rowscipy.stats.modecalls and preventing accidental in-place mutation of input labels. - Replace a fragile
tr | grepheader check with a field-basedawkcheck forsurfaceRAS.
Reviewed changes
Copilot reviewed 3 out of 3 changed files in this pull request and generated no comments.
| File | Description |
|---|---|
recon_surf/spherically_project.py |
Seeds Solver.eigs() RNG to make eigenfunction computation deterministic. |
recon_surf/smooth_aparc.py |
Avoids in-place label mutation and replaces scipy.stats.mode with np.bincount().argmax() for faster per-row mode voting. |
recon_surf/recon-surf.sh |
Uses an awk field match to robustly validate mris_info reports vertex locs : surfaceRAS. |
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Replace per-row scipy.stats.mode calls in sample_parc smoothing with np.bincount().argmax(), preserving scipy's smallest-label tie behavior for non-negative labels. Validation on 114823_MR1 against surf_speed_no_fs_t1_threads8_run1: mapped annotations byte-identical; final MRI volumes have zero voxel changes; white/pial/sphere.reg surfaces and morphometry have zero changes. sample_parc.py dropped from 61.57s total to 8.59s total; full wall time changed from 40:22.01 to 39:58.11.
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