Hi Spencer
Are 01.nii and 02.nii MRI volumes for different subjects? Do you have only a single volume/subject? If so, you would recon-all on each one individually. Something like:
recon-all -i <path_to_input_data>/01.nii -s subj01 -sdir <path you want to place your subjects> -all
if you have 8 cores and enough ram you can run 8 subjects at the same time, but you would probably need something like 32 or 64G of ram (can someone else comment on the ram requirements for a single recon-all?)
cheers Bruce
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Loong, Spencer Sent: Monday, June 21, 2021 2:55 PM To: Freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Recon-all for multiple cases
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Hello FreeSurfer specialists,
I am new to FreeSurfer and I am trying to learn how to run the basic recon-all command for multiple subjects at once. Could someone help me with what the command would look like to run a folder full of .nii files (e.g., 01.nii, 02.nii, 03.nii, etc). If I only have 8 cores, am I limited to running 8 cases per command, or can I include all of the cases (40) in the command? I’ve run the command for single cases successfully, now I would like set it and forget it.
Your help is greatly appreciated, thank you!
Spencer Loong Doctoral Student | Clinical Psychology Department of Psychology Loma Linda University SLoong@llu.edu
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