ENH: Implementation of FSL topup for DWI preprocessing

[sebastientourbier]

Following the issue #18 to integrate FSL topup correction (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup) in the diffusion pipeline

Tasks I see so far:

• Implementation of a new Nipype interface specific to FSL topup in cmtklib/interfaces/fsl.py OR an existing interface might be already implemented inside Nipype (not checked yet)

• Update of the interface to FSL eddy in cmtklib/interfaces/fsl.py which should now take as possible input the output of FSL topup.

• Update of the main subworkflow dedicated to the preprocessing of DWI data (in cmp/stages/preprocessing/preprocessing.py). Workflow should be updated or inputs/outputs of interfaces should be rearranged appropriately with the new OR modified interface in the function create_workflow of the class PreprocessingStage. Option for enabling/disabling should be added as a Boolean class attribute/trait to the class PreprocessingConfig.

Note: More parameters related to FSL topup itself must also be added there.

• If necessary, update the main diffusion workflow (in cmp/pipelines/diffusion/diffusion.py). This might involve updating outputs to be sinked to the main CMP3 outputs (<derivatives>/cmp/dwi).

• New attributes/traits can then be easily integrated and tuned in the graphical user interface by an appropriate update of the corresponding graphical component, implemented in cmp/bidsappmanager/stages/preprocessing/preprocessing.py