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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
CONFIDENTIALITY NOTICE: This e-mail communication and any attachments may contain confidential and privileged information for the use of the designated recipients named above. If you are not the intended recipient, you are hereby notified that you have received this communication in error and that any review, disclosure, dissemination, distribution or copying of it or its contents is prohibited. If you have received this communication in error, please notify me immediately by replying to this message and destroy all copies of this communication and any attachments. Thank you.
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
External Email - Use Caution
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
CONFIDENTIALITY NOTICE: This e-mail communication and any attachments may contain confidential and privileged information for the use of the designated recipients named above. If you are not the intended recipient, you are hereby notified that you have received this communication in error and that any review, disclosure, dissemination, distribution or copying of it or its contents is prohibited. If you have received this communication in error, please notify me immediately by replying to this message and destroy all copies of this communication and any attachments. Thank you.
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Fischl, Bruce -
Loong, Spencer