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

‐‐‐‐‐‐‐ 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?

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