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Hi Juan,

Thank you for the response! I did rename the file to ThalamicNuclei.v12.T1.FSvoxelSpace.mgz as you suggested, however I run into the following error when running trac-all prep in v7.3:

trac-all -prep -c /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/config/tracula_config.txt -noqa ...

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.v12.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

The file /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz was never created, which based on this response ( https://secure-web.cisco.com/13t_KJAXtZcpC_gOfCll4FYtVMXaIkjdLA8U-v2sJUFPyB8...) seems to be because of issues with using the mri/ThalamicNuclei.v12.T1.FSvoxelSpace.mgz file. I've attached my configuration file and the trac-all log, although this error section appears to be missing from the log file.

Any suggestions you might have would be greatly appreciated!

Best, Makenna

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

On Fri, Jul 29, 2022 at 7:53 AM Iglesias Gonzalez, Juan E. < JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:

Dear Makenna (and rest of users)

Thanks for spotting this bug, and for bearing with us while we transition to the new, Matlab-free code.

Renaming should be fine for now but we’ll certainly fix this on our end ASAP.

Kind regards,

Juan Eugenio Iglesias http://secure-web.cisco.com/1n-OaOnfhvsxFVcU07U1St5F0bdZPJNaj2ZTuvmVj-1O05DC...

On Jul 28, 2022, at 18:15, Makenna B McGill makennamcgill@utexas.edu wrote:

Hi FreeSurfer Developers,

I'm trying to run TRACULA in FreeSurfer v7.3 on OS Monterey.

I was unable to download R2014b Runtime on my newer OS, so instead of the segmentThalamicNuclei.sh script, I tried running the newer segmentation tool segment_subregions thalamus ( https://secure-web.cisco.com/1f16U4BOMTLy2zx3wBKG1xKc1x-zFBuasQvMGTtF9DhO_xA...).

This was successful, but trac-all looks for the ThalamicNuclei.v12.T1.FSvoxelSpace.mgz file, whereas the subregion segmentation produces the file ThalamicNuclei.FSvoxelSpace.mgz.

I'm wondering two things: (1) is the new segmentation tool compatible with trac-all (the wiki says the results will be very close but not identical), and (2) if so, would it be appropriate to rename/link the file so that trac-all can find it, as this user did with the ThalamicNuclei.v13 file ( https://secure-web.cisco.com/1l0V_ZXmXH4PpOQtIlZMcL5QAyjEqMHIFx7H2b-pJNep5zY... )?

Thank you in advance for any suggestions you might have, and please let me know if anything needs clarified.

Best, Makenna

*Makenna McGill *(she/her) Doctoral Student in Clinical Psychology University of Texas at Austin _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1Lz_LN-G3XZYoyXU61pbPxDebWNKi0ObcO4Mc9qEC1IexMr...

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