Hi Michael
First, in general you will always see differences between runs if something changes, like a mask that was waypoint becomes exclusion. This is because of the random number generation.
In your case, there is another source of difference, which is due to how waypoint and exclusion work.
Tracking proceeds along two opposite directions from the seed position. The two "half" streamlines can either be consider separately or in conjunction, and both can be useful in different contexts.
For exclusion, the two halves are considered separately. I.e. if one half goes through the exclusion mask, but not the other, we keep one half.
For inclusion (waypoints), you can either consider the two halves together or separately, using the option " --onewaycondition".
So imagine again that one half crosses the waypoint but not the other, then by default, the two halves get excluded. If you set "--onewaycondition", only one half gets excluded.
In terms of counting, a streamline is counted if either of its two halves is retained.
So you see from the above that "inclusion = not exclusion" only if you set the --onewaycondition.
Cheers
Saad
On 7 Dec 2012, at 18:49, Michael Harms wrote:
I was hoping someone could quickly explain the following.
Say I have a Thalamic seed mask with 1156 voxels, and I run probtrackx with Number of samples = 100
1) If I use no Target, then I get waytotal = 115600, which makes sense (1156*100)
2) If I use a Waypoint mask of a frontal ROI, I got waytotal = 18025
3) If I use that same frontal ROI as an Exclusion mask (and no other target masks) I got waytotal = 115262
Why is it that the waytotal values for (2) and (3) don't sum to 115600?
Or stated differently, I interpret (2) as indicating that 18025 streamlines hit the frontal ROI at some point but (3) seems to indicate that only 115600 - 115262 = 338 streamlines got excluded for hitting the frontal ROI when I used it as an exclusion mask.
thanks,
-MH
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Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
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Saad Jbabdi
University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466 (fax 717)