It's running quite a long time, with this repeating message: " This often happens because cerebellum or dura has not been removed from wm.mgz. This may cause recon-all to run very slowly or crash. if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freev... " I think the cerebellum and the dura seem to be ok: [cid:image001.png@01D82A5B.F7813420]
Any ideas? Thanks! Noam
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Peled, Noam Sent: Thursday, February 24, 2022 1:18 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Neverending mris_fix_topology
Thanks Bruce, I'm going to try that now.
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Fischl, Bruce Sent: Thursday, February 24, 2022 1:05 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Neverending mris_fix_topology
Hi Noam
Have you tried running it without -parallel? It looks like it is waiting for some other PID to finish Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto: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
