It looks like your recon-all was killed. Is it possible that your recon-all ran out of the job limit (time, memory, …).

I also noticed you have these options to recon-all ‘-3T -no-isrunning’. Make sure you don’t have other instance of recon-all running on the same subject.

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Lucas Alexis Ronat
Sent: Tuesday, February 6, 2024 12:21 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] ERROR: mri_ca_register with non-zero status 9

        External Email - Use Caution        

Hello FreeSurfer developers,

I'm trying to process structural MRI (T1w.nii) using the recon-all command but I get the following error: 

ERROR: mri_ca_register with non-zero status 9

Similar errors have been reported but I am unable to resolve this problem. Do you have any details on how to fix this? I have also attached the latest recon-all.log file in case it is useful. 

1) FreeSurfer version: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460

2) Platform: Alliance Canada Graham cluster (via MobaXterm terminal)

3) uname -a : Linux gra-login2 3.10.0-1160.88.1.el7.x86_64 #1 SMP Tue Mar 7 15:41:52 UTC 2023 x86_64 GNU/Linux

4) recon-all.log : see attached

I got a similar error on the Niagara cluster using FreeSurfer version 7.1.0 (ERROR: mri_ca_register with non-zero status 24)

Thanks for your help

Lucas Ronat

Postdoctoral Fellow

Douglas Research Center, Montreal, Canada