External Email - Use Caution

Hi Freesurfer Developers,

I'm trying to troubleshoot an error message during TRACULA preprocessing that seems to be related to the mri_binarize command used to create the /dlabel/anatorig/aparc+aseg+thalnuc.nii.gz file.

I'm using FS v7.3.2 on OS Monterey to run trac-all -prep and have attached both my configuration file and the log file.

Here is the error output:

7.3.2

cwd /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula

cmdline mri_binarize --i /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/aparc+aseg.nii.gz --min .5 --dilate 4 --erode 2 --o /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/aparc+aseg_mask.nii.gz

sysname Darwin

hostname PSYC-A30765

machine x86_64

user mbm3668

input /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/aparc+aseg.nii.gz

frame 0

nErode3d 2

nErode2d 0

output /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/aparc+aseg_mask.nii.gz

Binarizing based on threshold

min 0.5

max +infinity

binval 1

binvalnot 0

fstart = 0, fend = 0, nframes = 1

Found 1169534 values in range

Dilating 4 voxels in 3d

Eroding 2 voxels in 3d

Counting number of voxels in first frame

Found 1609388 voxels in final mask

Writing output to /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/aparc+aseg_mask.nii.gz

Count: 1609388 1609388.000000 16777216 9.592700

mri_binarize done

*printf: illegal option -- -*

*usage: printf format [arguments ...]*

*mri_binarize --i /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/t1prep/sub-0003107/mri/aparc+aseg.mgz --o /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz*

*ERROR: must specify minimum and/or maximum threshold or match values*

mri_concat --i /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz --i /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/t1prep/sub-0003107/mri/ThalamicNuclei.v13.T1.FSvoxelSpace.mgz --max --o /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz

ninputs = 2

Checking inputs

*error: niiRead(): error opening file /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz*

*ERROR: reading /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz*

mri_binarize --i /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/t1prep/sub-0003107/mri/aparc+aseg.mgz --match 2 41 7 46 172 177 77 --o /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/White-Matter.nii.gz

It seems like another user ran into the same issue ( https://secure-web.cisco.com/1udqzKCrR0Bj9BMcJxQpEnjsA37THUUcQftwPUH0tgkX_3M...). I've made sure that the mri/ThalamicNuclei.v13.T1.FSvoxelSpace.mgz file is in fact there (I appreciate the update that now looks for either v12 and v13), and I've also tried running trac-all -prep without the thalamic nuclei segmentation, which was successful. I know that including this segmentation is preferred for tracts near the thalamus, so any suggestions you might have for troubleshooting this issue would be greatly appreciated.

Let me know if there is any additional information I can provide.

Best, Makenna

*Makenna McGill *(she/her) Doctoral Student in Clinical Psychology University of Texas at Austin