Hi Noam

How much ram do you have in the machine? Is anything else big running? You can also examine that defect and see what is going on. 9000 vertices is pretty big so something significant like a chunk of skull might be fixable

Cheers

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Peled, Noam
Sent: Thursday, November 18, 2021 9:05 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all reconbatchjobs Segmentation fault

Thanks Doug!

Unfortunately, removing the parallel flag didn’t help:

“ …

After retessellation of defect 43 (v0=79551), euler #=-51 (145804,431777,285922) : difference with theory (-68) = -17

CORRECTING DEFECT 44 (vertices=9236, convex hull=4698, v0=79649)

Command terminated by signal 11

@#@FSTIME  2021:11:17:14:54:07 mris_fix_topology N 14 e 12788.52 S 1.14 U 12786.35 P 99% M 1761016 F 0 R 581366 W 0 c 79248 w 3 I 0 O 3960 L 1.01 1.00 1.00

@#@FSLOADPOST 2021:11:17:18:27:16 mris_fix_topology N 14 1.00 1.00 1.00

“

Any ideas?

Thanks again,

Noam

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Douglas N. Greve
Sent: Wednesday, November 17, 2021 10:09 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all reconbatchjobs Segmentation fault

I'm not sure what is happening. Does it work without the parallel flag?
btw, you are not using 7.2
here's your build: build-stamp.txt: freesurfer-linux-ubuntu18_x86_64-dev-20210824-e101185

On 11/16/2021 4:26 PM, Peled, Noam wrote:

Dear Freesurfer group,

I was running recon-all (Freesurfer 7.2 on Ubuntu) and received the following error:

“

 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 UC07 rh

Waiting for PID 6337 of (6337 6340) to complete...

Waiting for PID 6340 of (6337 6340) to complete...

/home/basuia/Documents/mmvt_root/freesurfer/bin/reconbatchjobs: line 77:  6340 Segmentation fault      (core dumped) exec $JOB >> $LOG 2>&1

PIDs (6337 6340) completed and logs appended.

“

Please find the log file attached.

Any idea what is the problem?

Thanks,

Noam

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