Hi Volker
If you are using B as termination, you should not see streamlines running out of B. It is more likely that these streamlines go past B without intersecting it, then come back to terminate in B.
An easy way around this is to have an exclusion mask past B. In your case, track from prefrontal, terminate+waypoint at Amygdala, and add an exclusion mask e.g. a single plane caudal to the Amygdala.
Cheers,
Saad
On 22 Dec 2011, at 13:20, Volker Baur wrote:
> Dear FSL experts,
>
> we are running probtrackx to do tractography between two ROIs A and B. We are only interested in the direct connection between A and B, so tried to use A as seed and B as termination mask. The problem is that there are still fibers running out of B into the opposite direction of A. Also we tried to use A as seed and B as waypoint AND termination mask. Has anyone an idea of which would be the best way to obtain only those fibers that are exactly between the two ROIs? For example, if we want to map tracts between a prefrontal ROI and amygdala, we are not interested in fibers running out of the amygdala to the occipital cortex.
>
> Also, is there a rationale of which of the two ROIs using as seed and which as termination mask?
>
> Thanks very much for any help,
> Volker
>
--
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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