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Hello Freesurfer Experts,
I am currently attempting to process a single subject via Tracula v7.2. Previously, I used v6.0 to process this same dataset through all three steps of Tracula (prep, bedp, and path) with equivalent parameters with no errors.
First, I ran recon-all -all on this subject which finished without error. Then I ran segmentThalamicNuclei.sh per instructions on the first page of the Tracula user guide - also finished without error. Then I passed the outputs of these steps onto trac-all -prep.
tract-all -prep exits with errors after about a minute. The command is unable to find the file aparc+aseg+thalnuc.nii.gz. This traces back to an error with mri_binarize:
mri_binarize --i /Users/user1/Desktop/QA_Tracula/recon-all-outputs/QA_subj/mri/aparc+aseg.mgz --o /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz ERROR: must specify minimum and/or maximum threshold or match values
aparc+aseg+thalnuc.nii.gz cannot be found because it is never created. However, all expected outputs previous to this file are created in the correct locations and trac-all -prep seems to be able to find all of the initial files I supply to it.
I've attached the full trac-all -prep output as well as the config file I used for full context.
Is there some threshold I need to specify in the config file? I looked at a complete example config file and I don't see any field related to this, but perhaps I'm missing something.
Or is this perhaps due to some error in my data? Any ideas?
Thank you!
Kayti Thorn (she/her) Database Specialist Medical University of South Carolina Department of Neurology Center for Biomedical Imaging 135 Cannon St. CS101 Charleston, SC 29425