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Freesurfer Experts,
I am trying to run mri_gtmpvc with the --rbv option, but am unable to progress, I always get a simple error immediately upon running:
Segmentation fault (core dumped)
The command I am running is this:
mri_gtmpvc --i FS_SPACE_pet.nii --reg-identity --psf 3.5 --no-rescale --seg ${SUBJECTS_DIR}/subject1/mri/gtmseg.mgz --default-seg-merge --auto-mask 1 .01 --o subject1_gtmpvcRBV.output --rbv
Things I have tried:
1. If I remove the --rbv tag, the command runs as expected. 2. If I run with the --rbv-res option, I still receive the error, even if I set the voxel resolution to a huge value e.g. 8 or 16. 3. My local machine has 32gb of RAM. If I try to run the command on our HPC cluster, I get the same error even when requesting 128gb of memory and 8 threads, using --threads 8.
I am running freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 on RHEL 9. The HPC cluster may have a slightly different version but has the same behavior.
Any thoughts on what I might be doing wrong here?
Thanks so much!
Houston Methodist. Leading Medicine.
Houston Methodist Hospital has been named the Best Hospital in Texas for patient care and quality for the 14th year in a row by U.S. News & World Report. We are proud to be a top-ranked hospital in the country, and nationally ranked in 10 specialties. For more than 100 years, we have been honored to provide you with the highest quality care possible. That’s the difference between practicing medicine and leading it. For you.
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