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_freeview

“

I think the cerebellum and the dura seem to be ok:

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.edu <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.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.edu <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.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