Also you need to use seeds to targets mode to replicate what was done in
that Rushworth paper. I don't think you need the 1D vector thing for what
you are doing, as that is for blind parcellations of a seed mask.
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Andreas Bartsch
Sent: Tuesday, June 22, 2010 12:49 PM
To: [log in to unmask]
Subject: [FSL] AW: [FSL] Gray matter parcellation using tractography
well, the toatl numebr of samples sent out is the number of samples sent out
from each voxel times the number of voxels. so you can use this as a
denominator. the waytotal is, strictly speaking, only to convert the fdt
paths output into <some> probability measure given you are sure that the
tract is there is each and every subject.
cheers-
andreas
________________________________________
Von: FSL - FMRIB's Software Library [[log in to unmask]] im Auftrag von
Massieh Moayedi [[log in to unmask]]
Gesendet: Dienstag, 22. Juni 2010 18:17
An: [log in to unmask]
Betreff: [FSL] Gray matter parcellation using tractography
Hi Everyone,
We've got tractography results from a gray matter seed for each of our
subjects. However, we are interested in doing a few things. I've read the
literature, and am still not entirely clear on the methods.
1) we'd like to quantify the data between groups (e.g., come up with some
sort of measure that will allow us to say whether 2 regions are more/less
connected between regions). I assume the way to do this is to run
tractography using a seed, and a waypoint mask, both of which are in the
same space. This puts out a waytotal text file.
However, if I want to get a probability distribution for each voxel within
the mask, how do I do this? For instance, Rushworth et al, (2005) state
that "for each voxel, the number of samples reaching a parietal target was
recorded as a proportion of the total number of samples going to all
parietal target areas." and further "For each target area, we then took a
mean value for all voxels in the seed area with any connectivity to that
target".
I'm not familiar on how to get the values 1) for each voxel, and 2) the
total number of samples.
In the Diffusion MRI book (Johansen_Berg and Behrens), the methods described
suggest to convert the the 3D Fdt image (tractogram) into a 1D vector- I
suppose this is another way to describe what's done above, but I'm not sure
how to actually do it.
thanks for your help-
Massih
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