[Mrtrix-discussion] tckgen: effect of signal amplitude and streamline length distribution

[Ulrike Kuhl]

Dear MRTrix team,

I use MRTrix3 to generate streamlines and SIFT for filtering the result. 
I noticed two things where I am not sure if the results are right.

a) I noted that my ODF glyphs appear to be huge when I load them into MRview (glyphs not being normalized to the b0 image, just as you propose). Even if I completely scroll out of the little ODF display window I am not able to see the corpus callosum glyphs completely. Likewise, I have to scale the overlay by at least 0.01 in order to distinguish individual glyphs. Is that normal?
If not, might it be ascribable to the fact that my data contains larger signal amplitudes than yours (you using TrioTim data with b = 3000; me using TrioTim data with b = 1000)? If so, do you see any problems that might arise when I use such huge glyphs for streamline generation and SIFTing?

b) Using my huge glyphs, I produce 10,000,000 streamlines with tckgen in the following way:

tckgen -algorithm iFOD2 -step 1.25 -samples 4 -maxlength 250 -number 10000000 -angle 45 -backtrack -force -seed_gmwmi GM_WM_interface.nii.gz -mask WM_mask.nii.gz -act 5tt.mif CSD.nii.gz out.tck

Plotting the histogram of resulting streamline lengths shows that by far the greatest proportion of these streamlines are really short (I attached histograms of streamline lengths before and after SIFT if you want to check out the distributions).
I go then on using SIFT to reduce the number of streamlines to 1,000,000 - also here, the greatest proportion are very short fibres. By visual inspection I noticed that there remains quite a number of short fibres in superior-inferior direction within the corpus callosum. That seems really wrong... does that correspond to the distribution of streamline lengths and location on your data after SIFT?

Thank you very much for your help,

Ulrike

-- 
Max Planck Institute for Human Cognitive and Brain Sciences 
Department of Neuropsychology (A220) 
Stephanstraße 1a 
04103 Leipzig 

Phone: +49 (0) 341 9940 2586 
Mail: kuhl at cbs.mpg.de 
Internet: http://www.cbs.mpg.de/staff/kuhl-12160 

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