Hi Saad,
Thank you very much for your swift service!!
Ifm trying to count the number of tracts that cross a particular ROI. The
most straightforward way to achieve this would be to set a ROI and count
the tracts that reached the ROI.
However, the default usage of FSL outputs the total number of counts
across all the voxels within the ROI, which does not necessarily reflect
the accurate number of the anatomical connections when one tract crosses
multiple voxels in the ROI.
It would be ideal if pathways stop as soon as they enter a termination
mask, instead of as soon as they leave a termination mask. I imagine the
algorithms of the two are quite similar and thus relatively easy to modify
but Ifm not good at programming in linux environmentc.
If you make your sphere a one voxel thick shell, it would still count
multiply when a tract proceeds along the margin of the sphere, which I
have often seen. Also, the use of an exclusion mask might help, but the
mask does not produce a proper tractography to present.
I would appreciate your thoughts.
Sincerely yours,
Junichi
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