The--onewaycondition flag doesn’t seem sensible with matrix3. AlsoI don’t know what your command was for doing the conversion. Here is the probtrackx2 callthat didn’t make it onto
the list:
probtrackx2 -x L.STS.fsl_MNI_new.asc --onewaycondition --omatrix3 --target3=L.STS.fsl_MNI_new.asc
In this case: seed region to whole brain connectivity. The STS seed is
mainly for testing purposes (not as many seed points as the whole WM), the
final analysis will use all WM voxels as seeds though. In fact,when I run
the analysis with WM as the seed the results look equally strange: only
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