[Mrtrix-discussion] Comparing methods: filtering full brain tracts vs. seeding specific tracts

[Dorian P.]

Hi all,

I am currently using MRtrix2 (yeah, I know is the old version) to do
tractography of the optic tract. I have success when using a seed (+ an
include roi + an exclude roi). However, when trying to select this pathway
from full brain tractography it does not work for me. The command
filter_tracks accepts only an include roi and an exclude roi. I  collapsed
my previous seed and include roi to obtain a new include roi for the full
brian filter. Yet, the result is not at all similar to the seed-based
tractography, with a lot of pathways not related to the optic tract.

Is there a way to use better the filter_tracks, i.e., to have more than one
include roi, such tracts are selected that pass both in roi1 AND in roi2.
The help of filter_tracks states "-include: Tracks that enter ALL  such
inclusion ROI will be included.". So doesn't seem to consider separate
portions of rois to get the tracks that connect them.

P.s. I am using Windows.

Thank you
Dorian
TJU
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