Hi,
I’m trying to generate a structural connectome using MRtrix in the native space of the subjects. I used Schaefer’s parcellation for the cortex, and Melbourne Subcortical atlas (S4: 54 regions, GitHub - yetianmed/subcortex).
The inverse warp of the antsRegistration call for native_to_mni registration was applied on the subcorticals to bring them to the native space (-n GenericLabel), however, there seems to be overlaps in some specific regions with the cortical ribbon (note the hippocampus below, white = ribbon).
I wonder if there are any solutions to avoid this overlap. I’m also interested to know your opinions and strategies to deal with this issue. For example, what I thought first was to assign those overlapping voxels to either the ribbon or the subcorticals by adding a few mathematical calculations.
Best,
Amir