External Email - Use Caution

Dear Freesurfer devs,

I would like to exclude from the T1 image those voxels that correspond to the cerebellum and brainstem. I tried to do this using the following commands although I am not completely sure if they are the right ones:

1. Extract cerebellum and brain stem labels from the aseg.mgz file

mri_extract_labels aseg.mgz 45 46 47 6 7 8 16 cerebellum_brainstem.mgz

2. Binarize the mask

mri_binarize --i cerebellum_brainstem.mgz --o cerebellum_brainstem_mask.mgz --min 0 --max 0

3. Convert the mask to native space

mri_convert -rl orig/001.mgz -rt nearest cerebellum_brainstem_mask.mgz cerebellum_brainstem_mask.nii

Any help would be appreciated. Thanks in advance.

Best regards,