Saad,
The loopcheck option is turned on when we are implementing probtractx.
I have tried to use the cortex and the medulla mask as a waypoint image. The
resulting tracts loook ok in the cortex, but very few of them descend down
to the brainstem, which does not follow known anatomical structure of the
corticospinal tract. Also, the values associated with the tracts range from
0 to 206, which is somewhat low given the total number of streamlines. Can
you suggest any other method for mapping the corticospinal tract so that the
fibers including those in the brainstem show up?
Also, I have used the option of multiple seed masks, using the posterior
limb of IC and cortex+brainstem as the two masks. The resulting tracts come
out looking correct, but the values are extremely low ( 0-12).
Could you explain the difference between using the waypoint masks and the
multiple seeding masks?
Thanks for your help,
Anastasia
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