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
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‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐
On Sunday, January 24, 2021 6:11 PM, Fischl, Bruce
<bfis...@mgh.harvard.edu> wrote:
Can you send us the full output?
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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?
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