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.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

You can't tell from the image whether the wm in cerebellum or dura is attached. you need to look at the wm.mgz volume to see. You can load the ?h.orig.nofix as well. In the terminal output of recon-all/topofix, it should give a vertex number of the topodefect. Go to that vertex n the nofix surface. That should get you close to the problem.

On 2/25/2022 3:25 PM, Peled, Noam wrote:

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:

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

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