Hi MRtrixperts, I’m running a single-shell fixel based analysis pipeline (following the relevant steps on the mrtrix documentation) on a dataset of around 300 or so images with 42 directions (b=1250). Upon inspecting the FODs created by dwi2fod, there seems to be unusually bright GM voxels in the …

This is expected: at this low b-value the signal intensity in GM exceeds that of WM, resulting in larger apparent fiber densities in GM than in WM

Just to add to this: You’ll find that the AFD in GM will be lower than in WM using higher b-values (nearer 3,000s/mm²), and these noisy lobes in the GM would be attenuated – another good reason to go for high b :wink: However, you might consider the use of a 2-tissue multi-tissue CSD approach here…

Hello going to high b is something we have difficulty to accept … the old habit … Just a precision about multi-tissue CSD for single shell (which is 2 shell with the B0) The advise is to run dwi2fod with WM and CSF. But the dwi2response have to run with the 3 argument (wm gm csf). Talking with T…

[image] Romain_Valabregue: The advise is to run dwi2fod with WM and CSF. But the dwi2response have to run with the 3 argument (wm gm csf). It’s not per se a “have to” for dwi2response, it’s just what those algorithms give you automatically (WM, GM and CSF response functions). But from an “in…

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FBA Single Shell - High GM FOD values

dwi2fod, fba

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