Hello MNE version 1.1.1 i tried to create bems via: import mne mne.set_config("FREESURFER_HOME", '/usr/local/freesurfer/7.3.2') mne.set_config("subjects_dir", '/usr/local/freesurfer/7.3.2/subjects') #subjects_dir = '/home/theuser/mne_data/MNE-fsaverage-data/fsaverage' subject = 'fsaverage' mne.b…

i tried this command in terminal: mri_watershed -useSRAS -surf /home/theuser/mne_data/MNE-fsaverage-data/fsaverage/bem/watershed/fsaverage /home/theuser/mne_data/MNE-fsaverage-data/fsaverage/mri/T1.mgz /home/theuser/mne_data/MNE-fsaverage-data/fsaverage/bem/watershed/ws.mgz and it worked! i guess…

mne.datasets.fetch_fsaverage() should download and expand automatically the files. you should not have to do anything manually regarding freesurfer is you have it setup when starting mne then mne should be able work while you stay in python Alex

Hi! Running into the same problem and was wondering if you found out how to run it through python?

mne.bem.make_watershed_bem compatablity with freesurfer 7.3.2

Support & Discussions

tbonesung (Dongjin Sung) April 12, 2024, 7:48pm 4

Hello! I was running across the same problems myself. Have you found out how to run mne.bem.make_watershed_bem in Python rather than in the terminal?
Thank you in advance!

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mne.bem.make_watershed_bem compatablity with freesurfer 7.3.2

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