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.

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Kaplan, Elizabeth <elizabeth_kaplan@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!