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