Hi Ellen
It is sometimes difficult to tell what an individual probabilistic streamline is actually doing.
I guess you may be able to clean up this tract by using an intermediate ROI in the internal capsule, exclusion masks where you think they should definitely not go, and perhaps play with the curvature threshold?
Saad
On 17 Oct 2011, at 21:16, Ellen Guller wrote:
> I've gathered from the list that, to get tracts that go only from ROI A to ROI B, and stop at ROI B, I should use ROI B as a waypoint and termination mask. When I do this, seeding in the cortex with a small thalamic mask as the waypoint\termination mask I still get some wispy tracts that seem to not really go anywhere. in addition, the tract going to the thalamus goes past the thalamus and into the temporal lobe. I can't tell it it is curving and coming back up to terminate in the thalamus. Is this normal for probtrackX or can I do something (besides play with the threshold) to increase the specificity of the tract?
>
> Thanks!
>
--
Saad Jbabdi
University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466 (fax 717)
www.fmrib.ox.ac.uk/~saad
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