>
Hi -
> I derived the transformation matrix using FLIRT using TI/ standard
> as my
> reference and the 3D volume B0 as my input the respective inverted
> matrix
> are plugged into the "transformation matrix" when i ran probtrack.
> (i.e for
> roi masks drawn on structural space, the inverted matrix
> "structodif.mat" is
> vice versa for standard space. However I'm puzzled why no tracts were
> generated as the seed masks are in close proximity to each other
> and are
> quite large in size.
>
The transformation to use is struct->diff and standard->diff, i.e.
from seed space to diffusion space, so your manips look correct to
me. Do you know if flirt worked well? (normally it does!)
So the only reason I can think of is maybe an error you may have done
manipulating the transformation matrices. Also make sure, if you have
any target points for your tractography, that all the rois are in
structural/standard space depending on which seed you are using.
cheers,
saad
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