[Freesurfer] mri_robust_template: Internal Error: Rotation should not scale.

[Sebille, Sophie]

Hi ,

I'm running Freesurfer's longitudinal pipeline and several of the participants 
generate the same error for the mri_robust_template step:
cmd: mri_robust_template --mov sub-ECTRO103-V1/mri/norm.mgz 
sub-ECTRO103-V2/mri/norm.mgz /sub-ECTRO103-V3/mri/norm.mgz 
sub-ECTRO103-V4/mri/norm.mgz --lta 
sub-ECTRO103/mri/transforms/sub-ECTRO103-V1_to_sub-ECTRO103.lta 
sub-ECTRO103/mri/transforms/sub-ECTRO103-V2_to_sub-ECTRO103.lta 
sub-ECTRO103/mri/transforms/sub-ECTRO103-V3_to_sub-ECTRO103.lta 
sub-ECTRO103/mri/transforms/sub-ECTRO103-V4_to_sub-ECTRO103.lta --template 
sub-ECTRO103/mri/norm_template.mgz --average 1 --sat 4.685

error: Internal Error for tp 2 -> template
 Rotation should not scale ( 1.44353e-05 )
 Debug Info:
A = [ ...
 0.9994648269692  0.0051381533060 -0.0325665649690
-0.0062826679505  0.9993709272221 -0.0351399801222
 0.0323652536320  0.0353254803840  0.9988599205733  ]

R = [ ...
 0.9994563704934  0.0051381078439 -0.0325662912834
-0.0062826179162  0.9993626623658 -0.0351396895455
 0.0323649840458  0.0353251881385  0.9988516601031  ]

S = [ ...
 1.084609181  0.29711 -0.43613
 0.29711  1.082701461  0.00049
-0.43613  0.00049  1.082701081  ]

Internal Error: Rotation should not scale.



Looking at the data, I don't see what could be the issue. Does anyone have any 
thoughts on this? I have attached the recon-all.log of one participant. I can 
also share the data if you'd like.

FreeSurfer version: freesurfer-linux-centos7_x86_64-dev-20200403-65d465d
Linux tonetti.nmr.mgh.harvard.edu 3.10.0-1062.4.3.el7.x86_64 #1 SMP Wed Nov 13 
23:58:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

Thanks,
Sophie


recon-all.log
Description: recon-all.log
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[Freesurfer] mri_robust_template Internal Error: Rotation should not scale

[Biles, Mandy K]

External Email - Use Caution

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



Thank you,
Mandy


Mandy K. Biles, MS | PhD Candidate

Psychology/Behavioral Neuroscience Program

UAB | The University of Alabama at Birmingham

CIRC Suite 252A | 1719 6th Avenue South | Birmingham, AL 35294

P: 205.975.4060 | mkbi...@uab.edu


uab.edu



recon-all.log
Description: recon-all.log
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