Hi Chris,

Are you setting the environment path correctly? It seems that infant_recon_all cannot find the relevant folder.

Best, Lilla
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Sayre, Christopher <csayre@vtc.vt.edu>
Sent: Wednesday, January 25, 2023 9:13 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Infant freesurfer issue
 

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Hello all,

 

I am having an issue when trying to run infant_recon_all. The error that I am getting is  /opt/apps/software/FreeSurfer.7.2.0-centos7_x86_64/bin/atlassubjects.csh No such file or directory.

 

I have searched through the bin folder          xç  xfor the atlassubjects.csh and indeed it does not exist. I have looked at the github for FreeSurfer and I was able to find the file under the infant folder. Am I missing something here or can anyone offer anything that would assist me in resolving this error?

 

Thanks,

 

Chris Sayre