Hi Sophie,
you can try using the --network option in probtrackx2.
This will give you a matrix (3x3 in your case) containing the number of streamlines between a seed region and each other ROI (note that they should all be specified as seeds). It will also give you a waytotal file containing the number of streamlines passing through at least one of the other seed regions when seeding from each one of them.
Combining these two information should get you the number of streamlines going from A -> B, bot directly and indirectly (i.e., via region C).
Hope this helps, cheers,
Matteo
> On 29 Nov 2017, at 20:19, Sophie Huang <[log in to unmask]> wrote:
>
> Greetings,
>
> I am interested in finding direct connections between two subcortical gray matter structures. Let's say A and B. However, I am concerned about indirect connections due to another structure, C. So I add in C as an exclusion mask. My results show very low connectivity between A and B after factoring in C. I understand that by adding in C as an exclusion mask, I may be getting rid of not only just fibers that terminate in C but also passing fibers (that don't terminate in C) to get to B. I know this is a long shot, but does anyone know if there are new methods out there that might possibly be able to distinguish between fibers that are just passing fibers from fibers that actually terminate in a structure?
>
> Thanks,
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