Tract overlap maps


I would like to be able to overlay my tracts on the same normalized scan so that I can see the degree of overlap in where they terminate (i.e. having a scale bar of intensity for the amount of overlap in the sample). I was wondering if there are any possible methods to generate overlap maps of the tracts generated from MRtrix.

I appreciate any help!

Thank you,

Hi Andrea,

It sounds like what you’re looking for is something akin to the technique that Shawna used in her paper. I’d have a read of that and see if it gives adequate guidance.

Probably the main decision to make is whether you will simply generate your maps in subject space then warp to template space, or whether to warp the tracks themselves to template space and then calculate the maps in template space (see the warpinit command). Once all of the images are transformed to / calculated in template space, the desired statistic can be derived; e.g. if you want the fraction of subjects for which the value is above a threshold, you could run mrthreshold separately for each subject, then use mrmath * mean out.mif to give the ‘mean value’ across the images (which is mathematically equivalent to the fraction of subjects for which the voxel is above threshold).

If you’re looking specifically for overlap in the streamlines terminations, this can be achieved using the same normalisation framework, but using tckmap -ends_only, such that the resulting maps represent the density of streamlines termination points specifically, rather than the streamlines themselves.