[QUESTION] dwi preproc

[arkiev]

DWI preproc workflow

Question

@Lestropie not sure if the preproc workflow is on your radar. Reckon you could take a closer look? I’m happy to help out, but I’ll need a bit of direction on what exactly needs to be done :)

[Lestropie]

Still trying to work through MRtrix3 PR list to get 3.1 done; will get to MRtrix3/mrtrix3#2665 eventually.
As noted in #448 there are some changes in MRtrix3_connectome that could be propagated:
bids-apps/MRtrix3_connectome#137
The main stumbling block when first working on the pipeline, being the manual volume-by-volume recombination within dwifslpreproc, is now resolved with the addition of dwirecon: MRtrix3/mrtrix3#2915
So the change within dwifslpreproc in that PR should be echoed in this pipeline.

I don't have a working environment with which to attempt to compile or execute the pipeline, which makes it very difficult to propose changes. If you can make the modification to include the use of dwirecon after eddy, and try to get it to a first compiling version, I can assist on debugging whatever gets spit out.