Dear mrtrix community,
I have generated whole-brain tractograms and segmented tracts of interest using inclusion and exclusion ROIs. Now, I would like to compute tract-specific scalar metrics (e.g., mean FA or mean MD of a given tract). I was wondering how to put mrtrix’s tools to best use to achieve this?
I tried three different methods. FA.mif is the FA map of the subject, tract.tck the tract of interest (in my case, the uncinate fasciculus), and binary_tract a binary mask of the tract of interest.
tcksample tracts.tck FA.nii.gz FA.csv -stat_tck mean
followed by the mean of all of the mean FA values of each streamline outputed by tcksample; or
tckmap -template FA.mif tract.tck FA_mask.mif mrstats FA.mif -mask FA_mask.mif -output mean
mrstats FA.mif -mask binary_tract.mif -output mean
As these three methods give me fairly different results (e.g. the mean FA of the UF ranges from 0.30 to 0.35), which one should be preferred? Or is the correct method not outlined above?