Hello Freesurfer Developers, 

 

I'm a medical student training with Freesurfer for my doctor thesis. My goal is to measure the brain volumetry of patients via SAMSEG. Attached is my logfile for run_samseg. 

 

 

When i run the samseg command: 

 

run_samseg --input STRUCT_samseg.nii.gz --output ~/fsl_course_data/registrat/SamsegOutput --threads 3

 

where: STRUCT_samseg.nii.gz is a T1 w image of a normal human brain.

 

 

It runs for a while an then gives me the message: 

 

Optimizer: maximalDeformation is too small; stopping

iterationNumber: 0

Killed

and just stops. There the files created as samseg output: 

samseg.talairach.lta  template_coregistered.mgz
cost.txt              template.lta          template_transforms.mat, 

 

 but not the stats file that estimates the volumetry of the brain. 

I've searched the forum but there weren't any similiar reports for this error. 

 

1) FreeSurfer version: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460

2) Plattform: Ubuntu 20.04.6 LTS 

3) uname -a: Linux TABLET-TSKI5C88 5.15.146.1-microsoft-standard-WSL2 #1 SMP Thu Jan 11 04:09:03 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux

4) log as text file is attached 

 

Last but not least I want to thank you for all your hard work! 

I really appreciate all the advice and support you give. 

 

 

Have a nice day, 

 

Marie