Hello FreeSurfer Developers,

 

I'm attempting to run the longitudinal pipeline for recon-all outside of fmriprep. The first step, cross, ran fine and I received the expected outputs. I started the base step and for most of my subjects it appears to be working but for some of my subjects I get the following error when running the mri_robust_template command:

 

 Internal Error for tp 0 -> template

 Rotation should not scale ( 1.23014e-05 )

 

I've searched the list and no similar errors have been reported outside of fmriprep forums that I can find. Does anyone have any thoughts on how to troubleshoot this issue? Also, I’ve attached the recon-all.log in case it's of any use.

 

1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

2) Platform: Red Hat Enterprise Linux Server, VERSION=7.7 (Maipo). This is being run on a HPC server.

3) uname -a: Linux c0072 3.10.0-1062.9.1.el7.x86_64 #1 SMP Mon Dec 2 08:31:54 EST 2019 x86_64 x86_64 x86_64 GNU/Linux

4) recon-all.log: see attached