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Dear MRtrixers,<br>
I've been using mrtrix for various things and came up with an
approach that I wanted to run by the experts. It might be that I'm
barking up entirely the wrong tree, so could use some guidance.
Regarding voxelwise metrics derived from the spherical deconvolution
(I saw the apparent fibre density (AFD) paper and this is something
I'd be interested in trying in the long run), I wondered whether the
largest FOD lobe might be sensitive to pathology. Here's my
analysis:<br>
<br>
Having run CSD (Lmax = 6, the b-value is only 1000, 42 directions)
on my data, I used find_SH_peaks, dir2amp and FSL's fslroi to
extract the FOD of the largest amplitude (I called this max_amp) and
thus was able to generate voxelwise max_amp maps per subject, in
native space. <br>
<br>
I then normalised the max_amp maps (by dividing by 3.5, to give a
scalar in the 0-1 range), having assessed the maximum amplitude in
any voxel across all subjects (which was 3.51ish). The idea being
that the the scalar now represents a score based on the amplitude of
the FOD lobe relative to the highest possible amplitude in vivo
tissue; thus 0 = absence of FOD and 1 = maximum possible FOD
amplitude.<br>
<br>
These normalised max_amp maps were then warped into group space
using the warps calculated from generating a groupwise template from
FA maps. I then created a mask using a threshold of FA>0.2 (to
limit analysis to white matter) and finally ran some stats (using
FSL randomise as per TBSS). In a group of 10 controls and 15
patients there were a number of significant clusters of increased
max_amp in controls, roughly corresponding to the corticospinal
tract and corona radiata. There were no increases in patients. <br>
<br>
The rationale behind this comes from the idea that the max_amp
metric represents the amount of diffusion in the principle
direction, but uncontaminated by crossing fibre effects (so perhaps
a 'better' version of axial diffusivity, I suppose). I'm not
assuming this idea is original by any means, perhaps just the
implementation of it in mrtrix.<br>
<br>
Apologies for the long post, but I'd be really appreciative of some
expert opinions. Any ideas for theoretical / practical improvements,
or reasons why this might not be representing what I think it is
would be most helpful.<br>
<br>
Many thanks,<br>
James<br>
<br>
<div class="moz-signature">-- <br>
<b>James Cole PhD | Research Associate | Huntington's Disease
Research Group | UCL Institute of Neurology</b></div>
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