I noticed all 292 images were processed in the same recon-all. I’m wondering if they are from the same subject.

If they are data from longitudinal study, you can process them with longitudinal pipeline - MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Iman Kianian
Sent: Saturday, August 26, 2023 9:52 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_watershed Error while running recon-all

External Email - Use Caution

Hi there,

I was trying to extract the hippocampus parts of a T1 MRI dataset with 292 samples as it is mentioned in the documentation ("MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala"). when I was trying to use the recon-all command, after almost 1 hour of processing I encountered this error:

"""

mri_watershed Error:
GLOBAL region of the brain empty !
Command exited with non-zero status 1

"""

I appreciate your time for helping me. Note that I attached the recon-all.log for your review if it is needed.