pybids_inputs_dwi doesn't provide snakebids CLI args for filtering

[akhanf]

This makes running the pipeline difficult without updating the config. I see the motivation for this, eg to deal with the case where dwi and T1w data are from two different bids datasets, but I actually think that doesn't happen too often in practice -- e.g. it won't happen for raw bids datasets (I know scattr doesn't deal with raw yet), and for preprocessed datasets e.g. snakedwi or others, there would be both T1w and dwi in the derivatives dataset.

So I am thinking the better solution is to place everything in pybids_inputs. Also could set some sensible defaults (the current defaults are pretty specific and almost always would need to be overriden).

[kaitj]

So I am thinking the better solution is to place everything in pybids_inputs

Agreed with this - the data was rarely (if ever) from two different datasets. It ended up splitting from a single pybids_input to deal with this when the bids and derivatives folders were at the same root-level rather than derivatives being a sub-directory within bids. I think when scattr was initially developed, only a boolean value was accepted for the derivatives parameter in the snakebids config. I believe it has been able to accept a list of paths to be added to the pybids index since, though how the config was being used here was never updated.

The derivatives flexibility should address the previous issue and should be able to move everything back under a single pybids_inputs.

[akhanf]

I've addressed this in #104, which should be ready to merge (perhaps after anyone is able to have a look, will go over in the scattr meeting today.