Not sure what is going wrong. Have you looked at your images? Eg, try
freeview orig.mgz aseg.presurf.mgz
It is a bit unusual that it is dying in two different places on the same data.

On 9/8/2021 3:39 AM, Falko Mecklenbrauck wrote:

        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
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