[Mrtrix-discussion] FOD amplitude

[James Cole]

Dear MRtrixers,
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:

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.

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.

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.

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.

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.

Many thanks,
James

-- 
*James Cole PhD | Research Associate | Huntington's Disease Research 
Group | UCL Institute of Neurology*
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