External Email - Use Caution
Dear Freesurfer Developers,
I'm attempting to compute the complete reconstruction of the
structural data of my participants.
Therfore I'm using the following commands through a
shell-script.
export FREESURFER_HOME=/usr/local/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
export FS_LICENSE= <path to license.txt>
SUBJECTS_DIR= <path to folder with nifti of
Subject>
inputFn1= <path to nifti-file>
outputDir= < path to output directory of
participant>
mkdir $outputDir
mkdir $outputDir/mri
mkdir $outputDir/mri/orig
outputFn1=$outputDir/mri/orig/001.mgz
mri_convert $inputFn1 $outputFn1
recon-all -s "<subject ID>" -autorecon-all
After trying the command a couple of times on diffrent profiles,
I'm always greeted with the message
"Command terminated by signal 11" without having a real ERROR
message.
I attached two recon-all.log files, where the process stopped on
mri_normalize and mris_place_surface respectively.
1) Freesurfer version:
freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551
2) Platform: Ubuntu 20.04.3 LTS (Codename: focal)
3) uname -a: Linux THALAMUS 5.4.0-81-generic #91-Ubuntu SMP Thu
Jul 15 19:09:17 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
4) both recon-all.log attached
(signal_11_mri_normalize_recon-all.log and
signal_11_mris_place_surface_recon-all.log)
Unfortunately the nifiti-File is to big to be attached. If you
need it, what would be the best way to share it with you.
Thank you very much in advance!
Best wishes,
Falko