DWI and SC updates: Complex data denoising

[PaulBautin]

PR for issue #154:

• add flag -dwi_phase. This flag allows for user to input DWI phase images (for the moment -dwi_phase image order must correspond to -dwi_main magnitude image order).
• use designer pipeline for denoising and removing gibbs ringing artifact.
• add flag to skip preprocessing (denoise + gibbs ringing artifact removal). This can already be skipped by having a preprocessed file in the output directory with name : dwi_corr="${proc_dwi}/${idBIDS}_space-dwi_desc-preproc_dwi.mif"
• Should we use single band reference images (sbref) for preprocessing?
• test if making even number of slices for FSL-TOPUP is still necessary

The code was tested with MRtrix 3.0.8.
However, the current container uses MRtrix 3.0.7, which contains a known bug in dwifslpreproc