Dear Ali, Making a SynthSeg version of the tool is on the to-do list but has not happened yet. For now, you need to run recon-all. The good news is that you get a ton of additional useful information on the brains! Kind regards, /Eugenio

-- Juan Eugenio Iglesias http://www.jeiglesias.com

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Ganjizadeh, Ali, M.D. Ganjizadeh.Ali@mayo.edu Date: Wednesday, December 27, 2023 at 22:04 To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Brainstem segmentation without pre-processing

External Email - Use Caution 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