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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hey Bruce, I’m helping a group from University of Cincinnati with this patient, so unfortunately I don’t have access to the data. They are running recon-all on a laptop that has 32 GB of RAM. Nothing else big is running in the background. Would you recommend manually fixing the defect in the skull?
Thanks, Noam
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Fischl, Bruce Sent: Thursday, November 18, 2021 9:29 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all reconbatchjobs Segmentation fault
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.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, November 18, 2021 9:05 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I certainly recommend looking at it and seeing what is causing it. Not sure if 32G of ram is enough or not, hopefully someone else can comment. The topology fixing space/time complexity is quadratic in the number of vertices, so 9,000 is getting pretty big
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Peled, Noam Sent: Friday, November 19, 2021 12:43 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all reconbatchjobs Segmentation fault
Hey Bruce, I’m helping a group from University of Cincinnati with this patient, so unfortunately I don’t have access to the data. They are running recon-all on a laptop that has 32 GB of RAM. Nothing else big is running in the background. Would you recommend manually fixing the defect in the skull?
Thanks, Noam
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, November 18, 2021 9:29 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] recon-all reconbatchjobs Segmentation fault
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.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, November 18, 2021 9:05 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Fischl, Bruce -
Peled, Noam