Hi Robert,
In my opinion:
A is fine.
B is equivalent to dividing by waytotal (condition on that particular tract), which is what we would recommend if you want the probabilities to be more comparable between subjects and less dependent on seed/target mask sizes.
C and D do not make sense to me...
It would be interesting to compare E and B, although in E I would also divide by waytotal to get around the target size issue.
Cheers,
Saad.
On 21 Oct 2010, at 20:38, Robert Schulz wrote:
> Dear FSL experts,
>
> having gone through quite a lot of older discussions I am still wondering what way would the best to work out voxel connectivity profiles. I am quite confused since I red that division by waytotal should be enough in unidirectional tracking.
> So if you don't mind, I'd like to explain my 5 actual approaches for connectivity probability of each spinal voxel to be connected to M1.
>
> just for information:
> downwward tracking = M1 seed mask (500 voxels, 5000 samles each) to spinal mask as classification mask
> upward tracking = spinal (230) to M1 classification mask
> waypoit masks: peduncular mask, spinal mask (in upward M1)
> extending exclusion mask (hemispheres, basal ganglia, cerebellum)
>
>
> Calculation of every spinal voxel connectivity probability is achieved via:
> -----------------------------------------------------------------------------------------
>
> A) (Spinal voxel's downward fdt_path value) / 500 x 5000
>
> B) (Spinal voxel's downward fdt_path value) / (only non-zero M1 voxels as read in downward's seed_to_spin x 5000)
>
> C) (Spinal voxel's downward fdt_path value) / (only non-zero M1 voxels as read in upward's fdt_path x 5000)
>
> D) (Spinal voxel's downward fdt_path value) / (only that M1 voxel that are non-zero as in B and (!) C x 500)
>
> The reason for approaches B-D was to exlude those M1 voxel from the normalization that were covered by the mask but are likely not sending and/or receiving paths to/from the spinal mask. To prevent undercorrection of the spinal voxel connectivity profiles.
>
> E) Simply upward-tracking, reading upward's seed_to_M1 voxel values / 5000. In this case, do I have to consider different cortical target mask sizes? Does they impact on tfhe spinal voxel connectivity probabilities?
>
>
> I would be very grateful if you could comment shortly on each approach. I know they are arbitrary, but I really want to consider as much as possible differing parameters to get robust probabilities.
>
> There are some more ways to calculate robust VCP I could think of (e.g. A x E, or further normalization for seed masks averaged FA), but for now I am confused enough. Can someone help me out here?
>
> Looking forward to your comments?
>
> Best
> 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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