Hi Elizabeth - This was a tricky one. My guess is that there's an error in what
comes right after the mri_binarize command, but the error doesn't get written
into the log file and is only shown on your terminal (I'm going to fix the
error logging aspect of this).
If my guess is right, the error comes when it looks for the thalamic nuclei
segmentation in the subject's mri/ directory. Is that there? Does this file
exist:
/autofs/cluster/lazar/Projects/DTIanalysis/Subjects_DTI_t1t2/AG010_1308_T1_LAZAR_recon.long.AG010_1308/mri/ThalamicNuclei.v12.T1.FSvoxelSpace.mgz
If that's the issue, you can run TRACULA without the thalamic nuclei
segmentation if you set usethalnuc = 0 in your config file. But if you're
interested in any of the tracts go into or near the thalamus, that's not
recommended.
Best,
Anastasia.
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Kaplan, Elizabeth
<elizabeth_kap...@brown.edu>
Sent: Monday, February 14, 2022 11:25 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Trac-all -prep -c error
External Email - Use Caution
Hello All,
I am attempting to process images using tracula, however I am running into an
error when attempting to run the "trac-all -prep -c" command line. Parcellation
was ran on FS 7.2.0, However, I am running the command on freesurfer dev
version due to an earlier resolved error reading index file:
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Trac-all exits on the command:
CMD mri_binarize --i
/autofs/cluster/lazar/Projects/DTIanalysis/Subjects_DTI_t1t2/AG010_1308_T1_LAZAR_recon.long.AG010_1308/dlabel/anatorig/aparc+aseg.nii.gz
--min .5 --dilate 4 --erode 2 --o
/autofs/cluster/lazar/Projects/DTIanalysis/Subjects_DTI_t1t2/AG010_1308_T1_LAZAR_recon.long.AG010_1308/dlabel/anatorig/aparc+aseg_mask.nii.gz
The Trac-all.log reads "mri_binarize done", see attached, and the outputs from
the mri_binarize command are present. I used the longitudinal configuration
file example on the wiki, attached below. Any guidance on how to navigate the
issue would be greatly appreciated!
Thank you!
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