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ENH: "Custom feature": Importing preprocessed data from BIDS Apps
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.
Related to support issue #38
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()
usingpybids
-
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 thepybids
query to get the inputs of the diffusion pipeline.
- Add
-
Preprocessing stage
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()
usingpybids
-
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 thepybids
query to get the inputs of the diffusion pipeline.
- Add
-
Preprocessing stage