[Mrtrix-discussion] Crossing-fibers gray matter CSD

[Wim Otte]

Hi Mrtrix-users,

In our lab we are setting up a procedure to determine structural
connectivity (voxelwize graph analysis) of gray matter voxels in rat
diffusion weighted imaging datasets (b-value 1200 s/mm2, snr 50,
directions 50, bzero images 2, voxelsize 0.5x0.5x0.5 mm3).
We know that the diffusion-tensor model is not appropriate in fiber
tracking gray matter voxels, so we want to use the constrained
spherical decomposition method.

However, I have some questions left (after reading the papers from
Tournier and Parker, Behrens).

- In which voxels do I have to estimate the fiber response function?
In all brain-voxels (resulting in a less 'flat' response function) or
in the white matter voxels? As we need it to track in both white
matter and gray matter voxels.

- How does streamtrack determine the principal tracking direction(s)
from the spherical decomposition data? Is it using a 'find_SH_peaks'
internally? Does it take crossing-fibers into account, or only the
first direction?

- tracks2prob flips my tracks in the x and y plane ( I have to
'correct' with fslswapdim -x -y z <input> <output> to get it right
with the 'reference image'). The fibers are oriented correctly in
mrview. Am I doing something wrong? (q-form, s-form thing?).

Thanks!

Wim Otte


-- 
PhD student
Image Sciences Institute
UMC Utrecht
wim at invivonmr.uu.nl