Can you send me your SUBJECTS_DIR, your command-line, and your working directory in a way that I can cut-and-paste them into the shell?

doug

Victoria Williams wrote:

Hi,

I have successfully run 126 subjects through bbregister and mri_vol2vol in order to translate the wmparc volume into TBSS space. However, there are 2 subjects that exited prematurely from bbregister. I think it may have to do with my naming system? 126 of the subjects have the subjid CVRAM_###_recon. But these 2 subjects that exited in error have 4 numbers: CVRAM_####_recon. I don't know how that would make a difference, but I've attached the bbregister logs. Although it doesn't say this in the log itself, in the terminal window right before it stops it gives me this message:

"Loading mov Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting LH Surfs Projecting RH Surfs Loading rh.white surf Loading rh.thickness Segmentation fault"

I'm running the following commands in the dev environment:

naming example: subject = CVRAM_####_recon (FS subjdir) basename = CVRAM_####

Commands: bbregister --s $subject --mov $DTI_DIR/${basename}_dti/preTBSS_0.4thresh-LAS/lowb-swap.nii.gz --dti --init-fsl --reg $DTI_DIR/${basename}_dti/${basename}_lowb-to-anat.reg

mri_vol2vol --targ $SUBJECTS_DIR/$subject/mri/wmparc.mgz --mov $DTI_DIR/${basename}_dti/preTBSS_0.4thresh-LAS/lowb-swap.nii.gz --o $DTI_DIR/${basename}_dti/${basename}_wmparc-in-lowb.nii.gz --reg $DTI_DIR/${basename}_dti/${basename}_lowb-to-anat.reg --inv --interp nearest

Thank you very much! Tori

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