Full processing pipeline with single phase-encoding direction in MS

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Hi Heena,

#Create mask (used this instead of the built-in ants/fsl options with dwi2mask as they were retaining substantial areas of the neck)

  • There are no ANTs / FSL options built in to dwi2mask; are you thinking of dwibiascorrect? Both of those algorithms will invoke dwi2mask if a brain mask is not explicitly provided, but the masking process itself is nevertheless done by MRtrix3.

  • Note that the prior dwi2response call will also invoke MRtrix3’s dwi2mask since a mask was not explicitly provided. You may want to confirm that the response function voxel selection was not influenced by errors in this mask.

  • In 3.1.0 the whole interface around DWI brain masking will change, which will make use of e.g. FSL’s bet2 a lot more convenient. See e.g. this page.

But as indicated with only 2 b-vals, I’m unable to estimate all 3 tissue types. So does that only leave below as an option?

What generally gets recommended in this scenario (but admittedly should perhaps be moved to the main documentation rather than scattered in various threads here) is to use the multi-tissue CSD algorithm, but provide only the WM and CSF response functions. This decreases contributions toward ODF magnitude from free fluid, and also utilises the hard-negativity constraint of that algorithm rather than the soft constraint of the original CSD algorithm.

This is the fod output. Is it too sparse?

It’s unclear exactly what you are referring to here as “sparse”. The FODs themselves are also too small to really assess properly; this is simply the size scaling that can be controlled via the ODF plot tool in mrview.

For the next steps, would it be better to use a freesurfer parcellation that was fed a binary lesion mask to improve segmentation (especially since I can’t perform distortion correction)?

I think there’s too many layers of ambiguity in this question for me to really be able to do anything with. It’s unclear how one would expect to use a FreeSurfer parcellation if EPI distortion correction cannot be performed, nor what the intended purpose of segmentation is.

Cheers
Rob