Hi MRtrix experts,
For a given parcellation, if I want to construct my structural connectivity (# of streamlines) with probabilistic tractography and SIFT2, is each entry of the final structural connectivity matrix normalized by ROI volume or surface area or no normalization at all? Thanks.
tck2connectome command will not apply any kind of normalisation or scaling that you don’t explicitly ask for. Normalisation by ROI volume (scaling by surface area is not implemented as we have not yet implemented surface data support across all relevant commands, though it would be pretty easy to do after the fact) is achieved through the
-scale_invnodevol option. Though I make an argument here as to why I’m generally opposed to such.