FIX: Move from smoothwm to white #806
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## master #806 +/- ##
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Coverage 62.28% 62.28%
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This was referenced May 18, 2023
mgxd
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May 18, 2023
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Sounds good. I don't think we'll need this for any maintenance releases of downstream tools. I think the reason was that I got white and smoothwm mixed up as to which was most refined ages ago. |
effigies
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Jun 6, 2023
…3011) ## Changes proposed in this pull request 1) Remove goodvoxels and CIFTI-specific code from `mri_vol2surf` resampling workflow. fsnative and fsaverage will remain the same for now. 2) Removes `fsaverage` as an implicit resampling target for `--cifti-output`. `fsaverage` and `fsLR` are now entirely independent. 3) Create a subject-specific cortical ROI mask in GIFTI space. Not currently output, as it's only needed internally; it's not a great mask but is intended to be more liberal than the fsLR mask applied later. 4) Adds a number of `wb_command` commands, including an OpenMP mixin that allows `OMP_NUM_THREADS` to be set in the environment. I think most commands can take advantage, but I only tagged slow ones (take >10s) that I could verify actually used them. 5) Depends on nipreps/smriprep#339 and nipreps/niworkflows#806. TODO: * [x] Restore literate workflow code. * [x] Restore saving goodvoxels mask, if desired. ## Documentation that should be reviewed TODO --- Closes #2990.
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We have some places where
wmis used for FreeSurfer surfaces instead ofwhite, breaking regexes/path building when usingwhitesurfaces.This PR also adjusts the (unused by anybody) gifti_surface_wf to convert white surfaces instead of smoothwm (see nipreps/smriprep#338), but that could be removed if we don't want to call that a bug fix.