Hi, I have a question regarding how to calculate FA for a tract.
I send 5000 fibers from a roi the thalamus to a certain cortical mask.
I obtain a tract with intensity values ranging from 1 to 22000.
I can average the FA over any voxel belonging to the tract, but this
weights voxels with very low probability of belonging to the tract the
same as those that are in the middle of white matter, so I think this is
wrong.
I can define the tract as any voxel with at least 50% probability of
connection to any voxel of my seed region, i.e. any voxel with at least
2500 fibers passing through. Do the FSL experts agree on this type of
threshold? This would be a "hard" segmentation of the tract.
I also can weight the FA at each voxel by the intensity of the tract
image (a "soft" segmentation). In this case, though, I think that a
ceiling should be imposed, i.e. that any voxel with a tract intensity >
5000 should be counted only once, while a colleague of mine thinks that
the proportionality should be maintained regardless of the nominal tract
intensity, i.e. that a voxel with 22000 fibers passing through should be
weighted 4.4 times one with 5000 fibers passing through. What is your
advice in this case?
Thanks for your help in advance. Stefano Marenco
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