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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