[Freesurfer] Brainstem segmentation without pre-processing

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Good evening, I am trying to work with segmentBS.sh. I want to pass my .nii.gz files that are already pre-processed with HD-BET, but I don't want to use recon-all as the first step because it takes a lot of time. I also tried recon-all -autorecon2 and 3, but it resulted in an error.

Is there any specific command that I will be able to pass my files directly to segmentBS.sh? Or is there any command for recon-all to only make subjects without processing or fast processing?

Thank you, Ali

Ali Ganjizadeh, M.D. (he/him)

Postdoctoral Research Fellow

Mayo AI Lab (Radiology Information Lab)

Mayo Clinic-Rochester