Hello MRtrix experts,
I am fairly new to MRtrix and am currently attempting to extract tracts between the left and right STN. I would like to eventually extend this to tracts between the STN and the motor cortex. I’m currently working with HCP data and used the DISTAL atlas included in LeadDBS to create the parcellation of the STN.
I tried running the following command for tracts between the left and right STN.
tckedit tracks_10M.tck -include lh.STN.mif -include rh.STN.mif STN_track.tck
Which successfully determined the tracts connecting the two ROIs, but only returned 10, which I don’t believe is correct.
I had previously attempted a similar procedure for the motor cortex, yet used the FreeSurfer atlas for the nodes. I used the following:
tck2connectome -symmetric -zero_diagonal -scale_invnodevol -tck_weights_in sift_1M.txt tracks_10M.tck T1w_parcels.mif T1w_parcels.csv -out_assignment assignments_T1w_parcels.csv
connectome2tck -nodes 23,72 -exclusive tracks_10M.tck assignments_T1w_parcels.csv moto
Which successfully determined the tracts and provided a lot more tracts between the nodes. I was trying to replicate this same procedure for the STN, yet it seems the DISTAL atlas files are probabilistic. I tried looking for a corresponding lookuptable (so as to be able to use labelconvert) but was unable to find it. Is my approach for the determining the tracts between the left and right STN correct?