I am trying to run probtrackx in FSL to detect structural connectivity between two ROIs. I have following two questions:

(1). The output fdt_paths.nii.gz is giving me some tracts other than those which are directly connected between these two ROIs. I used seed mask, termination mask, exclusion mask and waypoint mask as discussed here: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;72b22b08.1202

But I guess this previous post on this topic was without any conclusion.

So playing around with probtrackx, I noticed that tracks are getting limited between these ROIs if I keep reducing number of samples (in Options of PROBTRACKX window). Smaller the sample size better the results are. By default it has been set to 5000 which generates 900 tracts as shown in waypoint file (output) compared to if I set as 10 which generates 45 tracts strictly between 2 ROIs.

I was wondering if I can reduce the sample as low as 10 to generate tracks and report for publication purpose or higher the sample size better it is, even if tracts are out of between ROIs.

(2). Other than tracking # of tracts between these two ROIs, I am also interested in computing and reporting fractional anisotropy (FA) and mean diffusivity (MD) for these ROIs. I could not figure out how to generate FA and MD values here for publication purpose?

Thanks.