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Hell Freesurfers,
When running recon-all on a T1 image, I keep getting the error "Command terminated by signal 11" during mris_fix_topology. After manually editing brainmask.mgz and wm.mgz, I made sure that there were no larger defects and ran recon-all again. Still terminated by signal 11.
Next, I tried: recon-all -autorecon2 -autorecon3 -skullstrip -no-wsgcaatlas -s hires -clean-bm
:"Command terminated by signal 11". This time mris_fix_topology got through lh and got stuck on rh.
Any idea on what to try next?
Sent with [ProtonMail](https://secure-web.cisco.com/1WCB0vjqi1v_P1iPxErlGHm1UlxO4F8R6lzyInXC-taCfGX...) Secure Email.
Can you send us the full output?
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of KennethSPrice Sent: Sunday, January 24, 2021 5:01 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] command terminated by signal 11?
External Email - Use Caution Hell Freesurfers,
When running recon-all on a T1 image, I keep getting the error "Command terminated by signal 11" during mris_fix_topology. After manually editing brainmask.mgz and wm.mgz, I made sure that there were no larger defects and ran recon-all again. Still terminated by signal 11.
Next, I tried: recon-all -autorecon2 -autorecon3 -skullstrip -no-wsgcaatlas -s hires -clean-bm
:"Command terminated by signal 11". This time mris_fix_topology got through lh and got stuck on rh.
Any idea on what to try next?
External Email - Use Caution
Hell,
It appears that there is a large defect (6949 vertices) in rh but its not visible with freeview on wm.mgz.
Here is the output for recon-all -skullstrip -no-wsgcaatlas -clean-bm -autorecon2 -autorecon3
CORRECTING DEFECT 41 (vertices=6949, convex hull=1426, v0=38316) Command terminated by signal 11 @#@FSTIME 2021:01:24:22:39:31 mris_fix_topology N 14 e 397.87 S 0.82 U 396.68 P 99% M 705532 F 0 R 189055 W 0 c 0 w 0 I 0 O 0 L 0.52 0.58 0.59 @#@FSLOADPOST 2021:01:24:22:46:09 mris_fix_topology N 14 0.52 0.58 0.59 Linux DESKTOP 4.4.0-18362-Microsoft #1049-Microsoft Thu Aug 14 12:01:00 PST 2020 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s hires exited with ERRORS at Sun Jan 24 22:46:09 EST 2021
Best, Ken
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‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐ On Sunday, January 24, 2021 6:11 PM, Fischl, Bruce BFISCHL@mgh.harvard.edu wrote:
Can you send us the full output?
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of KennethSPrice Sent: Sunday, January 24, 2021 5:01 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] command terminated by signal 11?
External Email - Use Caution
Hell Freesurfers,
When running recon-all on a T1 image, I keep getting the error "Command terminated by signal 11" during mris_fix_topology. After manually editing brainmask.mgz and wm.mgz, I made sure that there were no larger defects and ran recon-all again. Still terminated by signal 11.
Next, I tried:
recon-all -autorecon2 -autorecon3 -skullstrip -no-wsgcaatlas -s hires -clean-bm
:"Command terminated by signal 11". This time mris_fix_topology got through lh and got stuck on rh.
Any idea on what to try next?
Sent with [ProtonMail](https://secure-web.cisco.com/1WCB0vjqi1v_P1iPxErlGHm1UlxO4F8R6lzyInXC-taCfGX...) Secure Email.
the topo fixer creates defect files that can help you find the error. I'm not sure whether they are created until the end, so they might not be there if there is a crash. You can try running defect2seg. If that completes, then you can look at the segmentation to see if that brings any clarity.
On 1/25/2021 7:50 PM, KennethSPrice wrote:
External Email - Use Caution
Hell,
It appears that there is a large defect (6949 vertices) in rh but its not visible with freeview on wm.mgz.
Here is the output for recon-all -skullstrip -no-wsgcaatlas -clean-bm -autorecon2 -autorecon3
CORRECTING DEFECT 41 (vertices=6949, convex hull=1426, v0=38316) Command terminated by signal 11 @#@FSTIME 2021:01:24:22:39:31 mris_fix_topology N 14 e 397.87 S 0.82 U 396.68 P 99% M 705532 F 0 R 189055 W 0 c 0 w 0 I 0 O 0 L 0.52 0.58 0.59 @#@FSLOADPOST 2021:01:24:22:46:09 mris_fix_topology N 14 0.52 0.58 0.59 Linux DESKTOP 4.4.0-18362-Microsoft #1049-Microsoft Thu Aug 14 12:01:00 PST 2020 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s hires exited with ERRORS at Sun Jan 24 22:46:09 EST 2021
Best, Ken
‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐ On Sunday, January 24, 2021 6:11 PM, Fischl, Bruce BFISCHL@mgh.harvard.edu wrote:
Can you send us the full output?
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *On Behalf Of *KennethSPrice *Sent:* Sunday, January 24, 2021 5:01 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] command terminated by signal 11?
* External Email - Use Caution *
Hell Freesurfers,
When running recon-all on a T1 image, I keep getting the error "Command terminated by signal 11" during mris_fix_topology. After manually editing brainmask.mgz and wm.mgz, I made sure that there were no larger defects and ran recon-all again. Still terminated by signal 11.
Next, I tried:
recon-all -autorecon2 -autorecon3 -skullstrip -no-wsgcaatlas -s hires -clean-bm
:"Command terminated by signal 11". This time mris_fix_topology got through lh and got stuck on rh.
Any idea on what to try next?
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Fischl, Bruce -
KennethSPrice