DWI pipeline to-do

[arkiev]

Things to implement in DWI workflow

• integrate dwifslpreproc (and code block associated with parsing filenames) from phantomkit
• currently handles a single atlas input; update to allow for multiple atlases (and generate multiple connectomes - will need to update output filename to reflect input atlas)

• need to organise outputs for all_parcs (T1 processing) and get DWI pipeline to parse all_parcs outputs appropriately
• add in tractography option to choose 5TT type (FSL, FS, HSVS)

• response function and FOD derivation- currently using subject response, but need to generate a study-specific response function
• investigate co-registration mismatch seen with BATMAN data
• FOD derivation: currently running MSMT; create a shell command task for SS3T and integrate into workflow. Make the CSD default, if single-shell do SS3T else do MSMT

[Lestropie]

There's been modifications to the origin tool subsequent to the initial porting that could be worthwhile integrating:
bids-apps/MRtrix3_connectome#137
Using the new denoising should be fairly straightforward to integrate.
The gradient non-linearity distortion correction would be nice to include, though I think I achieve it differently to how others do it.