Hi pt,

thanks so much for getting back to me so quickly and for helping me figuring this out! This is much appreciated.

So, by "Freesurfer annotation file with 300 parcels" I meant that I used an annotation file, extended the parcels into the WM, coregistered the resulting file to DWI space which then resulted in the parc300.nii.gz image.
How can I check if this file contains an integer at each voxel?

I forgot to mention that I also tried to use this command

@MakeLabelTable \
    -lab_file   labeltable.txt 1 0 \
    -labeltable labeltable.niml.lt \
    -dset       parc5002dwi_reo.nii.gz

before running 3dTrackID. This is how I know that some of the labels are being used to name the ROIs while the majority is listed with a simple integer (see attached png).

As you suggested, I ran the fat_mat_sel.py command. Trying to attach this image makes this homepage crash unfortunately (even after compressing it). Is there another way for me to send it to you?

I meant to also ask which outputs are also important to check, aside from the .grid file.
I tried

suma \
    -vol 3dTrackID_prob_000_PAIRMAP+orig[0] \
    -gdset 3dTrackID_prob_000.niml.dset

but this results in a funny image. Is there a better way of visually checking the streamlines and other output images?

Let me know what the best way is to get those files (parc300.nii.gz, .grid, .jpg output of fat_mat_sel.py, ...) to you and I will do that asap.

Thanks again!
Cheers,
Steph