FIX,MNT import surfaces generated from volumes with any voxel size#531
Merged
mvdoc merged 2 commits intogallantlab:mainfrom Apr 8, 2024
Merged
FIX,MNT import surfaces generated from volumes with any voxel size#531mvdoc merged 2 commits intogallantlab:mainfrom
mvdoc merged 2 commits intogallantlab:mainfrom
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OK, I tested this with a sub-mm T1, and it worked as well. |
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This PR fixes the bug first described in #300. Pycortex always assumed that the surfaces were generated out of T1s with 1mm3 isotropic voxel size. If one imported surfaces generated from other volumes (e.g., sub-mm), then the surfaces would be misaligned (see example in #300). To fix this issue, here I'm simply importing and converting the surfaces to gifti with Freesurfer's
mris_convert --to-scanner, which uses the same coordinate system as the T1 rather than the TKR system used for surfaces.This change produces the same surfaces as the old code for 1mm3 volumes. I'm waiting for freesurfer to finish on a sub-mm volume to test it there too.
(This PR also cleans up the code in that function a bit to make it easier to maintain...)