Hi Robert,
In multiple masks mode, the fdt_paths volume will contain the sum of all the fdt_paths that you would have got if you ran each seed separately, with the other seeds grouped as a single waypoint mask.
In general, the numbers in fdt_paths have the following meaning: what are the chances of hitting each voxel in the brain if I repeated the same streamline experiment through the diffusion field with a different noise realisation? It is the histogram of a spatial probability distribution discretised into voxels.
Using the various mask options in probtrackx can then be thought of as calculating a conditional probability.
For example, using a waypoint equates to conditioning on the streamlines going through a given region.
Combining the fdt_paths from A->B and B->A can be done using simple laws of probabilities.
For example, if you are interested in the probability of repeating the A-B OR the B->A experiment at a given voxel, you can write:
p(A->B OR B->A) = p(A->B) + p(B->A) - p(A->B AND B->A)
where if you assume that the two events are independent (which is probably not true!):
p(A->B AND B->A) = p(A->B)*p(B->A)
However, before doing all this you need to normalise each of the distributions (divide by waytotal in each case).
I hope this is not too confusing,
Cheers,
Saad.
On 18 Oct 2010, at 09:28, Robert Schulz wrote:
> Hi FSLers,
>
> again, thank you so much for your recent helpful answers. Targeting voxel connectivity profiles of the medulla up to different motor areas, I am recently wondering the following: I am sucessfully testing both downward and upward tracking with classification masks (medulla and cortical, resp.) and use different approaches for normalization (seed-to. etc...) answering different questions.
>
> Although I read about multiple mask approach for robust bidirectional tracking, it's not 100% clear to me what the numbers in multiple-masks' fdt-path mean?
>
> My question?
>
> What do the numbers at the medullar mask voxels mean? If I have 300 voxels in this seed/target mask and 5000 samples each (and for instance 400 M1 voxels in the second mask), what is the according denominator for calculating connectivity profiles? How do I use multiple-mask for this approach? What does the number really mean?
>
> Thank you very much for your answers!
>
> Kind regards to you
>
> Robert
>
--
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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