Hi Saad,

Thank you very much for your swift service!!

I’m 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 I’m not good at programming in linux environment….

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