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, -- *Miguel Ángel Rivas Fernández*
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