L.S.,
I'm using probtrackx2 (FSL 5.0) with the --omatrix options to create a full-brain connectivity matrix. As seed voxels I use those voxels that are on the boundary of grey and white matter. Using --omatrix1, I then obtain an NxN sparse matrix of streamlines. However, I assumed that each row would sum to P - the number of drawn streamlines per seed voxel - so that dividing this row by P would yield the proportion of streamlines that end up somewhere. It turns out that probtrackx does not stop when a seed voxel is reached, so that the counts for all voxels under the streamline are increased. So basically, if A is connected to B, and B to C, A will also show streamlines to C.
Is it possible with the current FSL options to obtain a NxN matrix that contains only streamlines that go directly from one seed voxel to another, without intermediate stops?
Thanks for your help!
Max
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