FBA measures for specific tracts per subject

#1

Hi all,

Apologies if the answer for this have been covered elsewhere but I’m going around in circles a little trying to come up with the right command/s to do this.

Using ROIs and tckedit I’ve delineated a number of specific streamlines (tcks) from the whole-brain tractography (generated via a study specific wmfod template and tckgen).

How to I go about creating a mask for each of these trk files so I can to calculate the mean value of FD within this mask for each subject via the mrstats command?

#2

Ugh. I got it. Just for future reference for anyone…

tck2fixel will convert the tck to a fixel .mif image
eg tck2fixel tract.tck fdc fdc tract.mif
(two “fdc” are the folders containing the directions and index.mif’s the command requires. It can be any folder with these files in them

then

mrstats using this tract fixel image for the measure of interest.
eg foreach * : mrstats IN -output mean -mask tract.mif

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