Dear MRtrix experts,
we are currently working on tractography to small subcortial subnuclei. For example in the thalamus, some nuclei are quite small (only some mm) and are directly attached to each other.
As expected, we found that if we change the
tck2connectome -assignment_radial_search ‘radius’
we change the number of streamlines assigned to those nodes.
If we work with a liberal radius of 2 or 1 mm, which provides good results for our cortical fiber count, the subcortical fiber count of the small nuclei seems to be a bit high. We guess that especially small nuclei will ‘benefit’ from the search radius around them.
If we reduce the search radius to 0.5 mm, we get a huge decrease of fiber count for both the cortical and subcortical elements. For the cortex, 0.5 mm may be too conservative because of the 5TT definition of streamline ending points, but we guess, for the small subcortical elements, this radius should be more reliable, since the nuclei generelly are quite small (and the 5TT file definition should be less a problem in our opinion, see below).
The question to you is - despite of the idea of using more advanced ACT techniques like ‘Mash based ACT’, what is your experience with small nuclei.
Second, in my understanding of ACT, the fibers into the tissue with the definition of subcortical gray matter in the 5TT file, will go ‘into’ and end ‘within’ the tissue and not end at the border of the area like at the cortex. For that reason, it should be possible to extract the fiber count to any subdivision of subcortical regions by simply further subdividing the ‘input node parcellation’ file for the tck2connectome command and consequently extract the fiber count to the subdivisions only. Some confirmation would be apprechiated :).
Best wishes, Tom