Running FastSurfer as MacOS package

Installation Instructions

If you want to run only segmentation (replace placeholders starting with “<” and ending with “>”, see https://deep-mi.org/FastSurfer/stable):

run_fastsurfer.sh --seg_only --sd <path/to/output/dir> --sid <subject_id> --t1 <path/to/subjects/t1/image>

To run the full FastSurfer:

run_fastsurfer.sh --device mps --sd <path/to/output/dir> --sid <subject_id> --t1 <path/to/subjects/t1/image> --fs_license </path/to/freesurfer/license>