Hi Robert,
> Option 1) For corticospinal tracking, I track from cortical seed mask to spinal target mask, and have a peduncular waypoint mask. For determining connection probability and further visualization / voxel connectivity profiles, I prefer reading out the fdt_path hits/waytotal at the peduncular mask, not at the spinal. Is this a possible way?
waytotal will give you the number of samples that made it to the waypoint mask, regardless of where it goes afterwards. So if you are only interested in connections that go all the way to the spinal target, and include the peduncle as a prior on where the trajectory goes through, you should include the spinal target as a waypoint (together with peduncle).
I am not sure what you mean by "reading out fdt_paths". fdt_paths gives you a voxelwise information about waytotal, so it is a bit trickier to read out within an ROI mask (as a given sample can go through more than one voxel within the ROI).
> Option 2) Again, corticospinal tracking in the following way: Cortical seed mask, peduncular class target. Waypoint masks are both ped and spinal mask. FDT values/waytotal are read out at the peduncular mask.
See (1).
Cheers,
Saad.
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> Both ways give similar results. To your opinion, can I continue these ways?
>
> Kind regards and thanks for your comments
>
> Robert
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--
Saad Jbabdi
University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466 (fax 717)
www.fmrib.ox.ac.uk/~saad
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