Hello all,
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.
- FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
- Platform: Red Hat Enterprise Linux Server, VERSION=7.7 (Maipo). This is being run on a HPC server.
- 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
Here is the relevant parts of the log file.
Input rotation’s max deviation from rotation is: 2.55908e-05
computing mean coord of TP 2 ( /scratch/mkbiles/PVTS/PVTS_reconall/PVTS105.post/mri/norm.mgz )
mapping back to rot, err = 3.42194e-16
computing mean coord of TP 1 ( /scratch/mkbiles/PVTS/PVTS_reconall/PVTS105.pre/mri/norm.mgz )
Internal Error for tp 0 -> template
Rotation should not scale ( 1.27952e-05 )
Debug Info:
A = [ …
0.9997053452569 0.0153968624045 0.0183728667127
-0.0154472707138 0.9998698955838 0.0026049766111
-0.0183305045360 -0.0028880402300 0.9998203412904 ]R = [ …
0.9997126416857 0.0153969742788 0.0183730029359
-0.0154473854225 0.9998772886115 0.0026049956697
-0.0183306393079 -0.0028880619603 0.9998278085554 ]S = [ …
0.9999927014255 0.0000000019624 0.0000000009901
0.0000000019624 0.9999926060941 0.0000000004122
0.0000000009901 0.0000000004122 0.9999925314683 ]Internal Error: Rotation should not scale.
Linux c0068 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
recon-all -s PVTS105.average exited with ERRORS at Thu Jan 23 13:06:27 CST 2020
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting