Hi Paul,
I’ve sent you some answers, but just in general for others: it’s important to distinguish 2 separate challenges here. The first is to get a good bundle definition. A few tricks related to your scenario are also found at Obtain tract segment using tckgen/tckedit ; but in general, it requires some playing around with various tricks to get the result you’re after. The -stop option will in most scenarios be useful here, as long as you can work with the fact that it stops streamlines upon entering the inclusion region, rather than tracking in and stopping upon attempting to exit. For most WM analyses, that can make good sense though, depending on how your inclusion regions are defined or obtained.
The second challenge is how to get a fixel mask from these streamlines. That’s generally done via tck2fixel to map the streamlines, followed by mrthreshold with a well considered -abs value to obtain a binary fixel mask. There’s a few other minor cleaning steps that can be added among these commands, but generally, that’s the gist of it.
Such a binary fixel mask can then be used via fixelcfestats, but only if you’re still after a per-fixel stat within the mask. At this stage, many people might however be after a fixel-region average metric, and stats on that across a population. mrstats can get you those averages, when supplying it via -mask with your fixel mask. In that scenario, stats can/will be done using any external software that suits you.
Cheers,
Thijs