Hi -
can I just confirm - I think that if I define a seed mask and a target mask and set e.g. --omatrix3 then if a track intersects the target masks multiple times, each intersection will generate a fresh entry in the output matrix?
the behavior I'm looking for is to count only the first intersection. Making the target a stop mask won't work in this case. the seed is a surface of the entire gray matter. the target is a surface of the entire grey matter a very small distance deep to the seed.
what's being tested is not intersection with the target mask. the output matrix is assumed to be an identity matrix pretty much. the subsequent test on the tracks once they enter the WM decrements the matrix entries by discarding tracks that don't pass a test.
i.e. I'm trying to make a map on the surface of how many tracks seeded from each node pass the test, and plot the map on the surface.
So to get the behavior I want it occurs to me that I could simply discard entries in the output matrix that are far from the diagonal.
or, rather than use a surface as the target I could fill the target surface with voxels. it should then be hard for a track to enter it more than once. The disadvantage of that approach is that it'll be harder to tell if there have been multiple intersections (there could be potentially).
Is there a smart (ideally computationally efficient) way to get the behavior I want (for each seed node, count how many of the seeded tracks are not discarded by a test of some sort, plot those numbers as a surface)
thanks,
Colin
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