Description of the problem
It appears that Freesurfer 8's shift to synthstrip by default no longer generates the talairach_with_skull.lta file necessary for bem.make_watershed_bem to run with gcaatlas=True. The missing file can be created by running the following command.
mri_em_register -skull nu.mgz /usr/local/apps/freesurfer/7.4.1/average/RB_all_withskull_2020_01_02.gca transforms/talairach_with_skull.lta
Not sure whether we should add this step as a check in the function and run before the mri_watershed or perhaps just check if the file exists and then advise user to run the command separately on failure.
Steps to reproduce
- Run Freesurfer v.8.0:
recon-all -s {subj} -I {dicom_path} -all
- attempt to run watershed from python with gcaatlas:
mne.bem.make_watershed_bem(subject, sourcepath, overwrite=True, atlas=True, gcaatlas=True, show=True)
- Note missing file:
{subj}/mri/transforms/talairach_with_skull.lta
Link to data
No response
Expected results
Function mne.bem.make_watershed_bem when given gcatlas=True would run mri_watershed and create the BEM.
Actual results
Function mne.bem.make_watershed_bem when given gcatlas=True fails.
Additional information
I can probably do a PR to fix, just curious how everyone feels about 1. should we run the mri_em_register for the user if file is missing or 2. error out and advise them to run command?
Description of the problem
It appears that Freesurfer 8's shift to synthstrip by default no longer generates the
talairach_with_skull.ltafile necessary forbem.make_watershed_bemto run withgcaatlas=True. The missing file can be created by running the following command.Not sure whether we should add this step as a check in the function and run before the mri_watershed or perhaps just check if the file exists and then advise user to run the command separately on failure.
Steps to reproduce
recon-all -s {subj} -I {dicom_path} -allmne.bem.make_watershed_bem(subject, sourcepath, overwrite=True, atlas=True, gcaatlas=True, show=True){subj}/mri/transforms/talairach_with_skull.ltaLink to data
No response
Expected results
Function
mne.bem.make_watershed_bemwhen givengcatlas=Truewould runmri_watershedand create the BEM.Actual results
Function
mne.bem.make_watershed_bemwhen givengcatlas=Truefails.Additional information
I can probably do a PR to fix, just curious how everyone feels about 1. should we run the
mri_em_registerfor the user if file is missing or 2. error out and advise them to run command?