I am trying to use MRtrix for subcortical structure parcellation (i.e.,GPi), and currently having some issues. Just wondering if anyone can kindly share their experience on the similar topic.
The way I try to obtain the functional subdivisions is by generating the streamlines (5k/voxel) for the seeding ROI (ie. GPi) and the target region (a functional cortical region). The process is repeated for each functional cortical regions of interest. Then, by converting the resulting .tck files into tdi (I also saw others use the streamline end points map), I use the winner-takes-all approach to determine the sub-regions within the nucleus.
I understand that the streamlines should really run through the white matter regions. The tdi I obtained seem to only lean near the interface of GPi and whiter matter, but the opposite side towards other subcortical nucleus is not receiving any streamlines for parcellation purposes…this accounts for about half of the GPi volume.
I am wondering if there is any step that I missed, or additional processing I should perform to deal with this issue?
Thanks a lot!