Hello MRtrix team,
I’m pretty new to MRtrix and MRI image processing in general. I’m trying to use MRtrix to generate a structural connectome from the Human Connectome Project for further analysis in The Virtual Brain, but it requires a lot of components for it to work.
Specifically, I need the connectivity weights, tract lengths, region center coordinates and labels, region orientations, region areas, cortical flags, and hemisphere flags.
I followed the ISMRM tutorial to get the actual weights matrix. Then I was able to generate the tract lengths from tckstats. I ran one of the custom functions posted on another topic,
mrcentre.cpp to generate the region centers. The region labels and all the flags I was able to extract from the
fs_default.txt file. But I am struggling to figure out how I can calculate the region areas and orientations. What functions will I need to run to get that?
The Virtual Brain defines areas and orientations as follows:
Areas: Estimated area represented by the regions in the connectivity matrix.
Orientations: Unit vectors of the average orientation of the regions represented in the connectivity matrix.
Really appreciate any assistance!