Hi Noam Have you tried running it without -parallel? It looks like it is waiting for some other PID to finish Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Peled, Noam Sent: Thursday, February 24, 2022 12:36 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Neverending mris_fix_topology Dear group, I'm trying to run recon-all (freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551) on my Martinos' desktop. I killed it after waiting quite a of time for the mris_fix_topology to be completed: Waiting for PID 225967 of (225964 225967) to complete... What can I do to be able to process this subject? I attached the recon-all log. You can also find all the logs here: /autofs/space/mmvtclin_001/thibault/1/users/npeled/subjects/UN07/scripts Thanks! Noam
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