I’m interested in the centers of the regions for which the connectome is estimated. To do so, I’m using the labelstats in scanner space. I would like to ask in this case, how the centers are estimated and in what units are they expressed?

I have another question regarding the distances between the regions as measured with tck2connectome. What units do the estimated distances have? Also, I have quite a few off-diagonal zeros in the distance matrix, is that normal?

Thanks a lot for your time and help.
Best Regards,
Mahta

They are computed as centres of mass, which basically means the average position of all voxels in each parcel. They’re expressed in millimeters relative to isocentre, in scanner coordinates (unless the -voxelspace option is used).

tck2connectome does not measure distance as such. It reports on some measure of ‘connectivity’. Given the vast number of options available to compute various metrics, it’s impossible give a single answer to that question – I’ll have to refer you to the documentation here.

Yes, that’s what you’d expect since it’s unlikely that any tractogram will contain streamlines connecting between all possible pairs of regions. In fact, one of the most common criticisms of probabilistic tractography (the default in MRtrix) is that it generates too many false positives – which implies that the resulting connectome would be expected to have more zeros in it…