Hello
The dip mostly corresponds to pyramidal tract connections from the motor cortex. The more unconstrained you leave tractography the more connections you will get. A good way to increase specificity in this example would be to use a midsaggital corpus callosum mask as a waypoint and an internal capsule mask as an exclusion.
Cheers
Stam
On 9 Dec 2013, at 16:24, Thushini Manuweera <[log in to unmask]> wrote:
> Hello!
>
> I am currently running tractography for stoke patients, using the contralesional motor cortex(Mc) as the seed, motor area of the corpus callosum as the waypoint mask and the ipsilesional motor cortex(Mi) as the termination mask. When I run the tractography I get a dip in the tracts originating from the seed before going in to the corpus callosum as shown in the attachment. However when I ran the tractography for the same patient using the Mi as the seed and Mc as the termination mask, I do not see the dip in the tract seen in the previous tractography going from Mc to the corpus callosum. Although I do see a small dip in the tract in the second tractography, going from Mi to Mc (Mi set as seed). Would this dip in the tractography be considered acceptable? Or should I be using a exclusion mask?
> And I am also thresholding the normalized tractography using 0.00004 as my threshold. Would this be considered a good setting?
> I would really appreciate it if someone could please help me out.
>
>
> Thank you in advance!
> Best regards,
> Thushini
> <MctoMiARN_10_24.JPG>
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