ENH: "Custom feature": Importing preprocessed data from BIDS Apps

[sebastientourbier]

While adopting BIDS in CMP3, the way CMP is working changed dramastically and this feature, available in previous versions, is not working anymore for the moment.
However, this is an important feature but this would also require to rethink the way the "custom" feature is working, such as working with BIDS derivatives directories obtained for instance by smriprep / dmriprep or fmriprep.

[sebastientourbier]

Related to support issue #38

[sebastientourbier]

Such a functionality would require for:

Diffusion pipeline

• To specify a custom BIDS derivative directory with preprocessed diffusion MRI data that contains *_desc-preproc_dwi.nii.gz / *_desc-preproc_dwi.json / *_desc-preproc_dwi.bval / *_desc-preproc_dwi.bvec files

• Input file availablity would be checked in check_input() using pybids

• The files would be retrieved using BIDSdatagrabber

• New config traits

  • Preprocessing stage
    • Add use_custom_bids_derivatives boolean trait
    • custom_bids_derivatives that specifyies the BIDS derivatives directory where preprocessed diffusion data is located.
    • pybids_config a path to a JSON file that specifies the pybids query to get the inputs of the diffusion pipeline.

Functional pipeline

• To specify a custom BIDS derivative directory with preprocessed functional MRI data that contains *_desc-preproc_bold.nii.gz / *_desc-preproc_bold.json files [TO BE UPDATED]

• Input file availablity would be checked in check_input() using pybids

• The files would be retrieved using BIDSdatagrabber

• New config traits

  • Preprocessing stage
    • Add use_custom_bids_derivatives boolean trait
    • custom_bids_derivatives that specifyies the BIDS derivatives directory where preprocessed fMRI data is located.
    • pybids_config a path to a JSON file that specifies the pybids query to get the inputs of the diffusion pipeline.