Module: io_bids
Subworkflow loading files from a BIDS directory. It is used in conjunction with the IO_READBIDS module which uses the scilpy CLI script to parse the BIDS directory and fetch the metadata. ------------- Current supported files/metadata ------------- Files:
- T1w
- White matter parcellation from FreeSurfer.
- Grey matter parcellation from FreeSurfer.
- Diffusion weighted images (dwi)
- B-values (bval)
- B-vectors (bvec)
- Reverse encoded diffusion weighted images (rev_dwi)
- B-values for the rev_dwi (rev_bval)
- B-vectors for the rev_dwi (rev_bvec)
- Reverse b0 image (rev_b0) Metadata (within the meta):
- Subject ID (id)
- Session ID (ses)
- Run ID (run)
- DWI Total Readout Time (dwi_tr)
- DWI Phase Encoding Direction (dwi_phase)
- Reverse DWI Phase Encoding Direction (dwi_revphase)
Note: This subworkflow is meant to be an example of how to use the IO_READBIDS module. It only supports a single BIDS folder as an input. It can be modified to fit the user’s needs.
Inputs
| Type | Description | Pattern | |
|---|---|---|---|
| bids_folder | directory | Path to the BIDS directory. (You must supply only a single BIDS directory) Structure: [ path(bids_folder) ] | |
| fs_folder | directory | Path to the FreeSurfer directory. Structure: [ path(fs_folder) ] | |
| bidsignore | file | Path to the .bidsignore file. Structure: [ path(bidsignore) ] |
Outputs
| Type | Description | Pattern | |
|---|---|---|---|
| ch_t1 | file | Channel containing all T1w files Structure: [ val(meta), path(t1) ] | *.nii.gz |
| ch_wmparc | file | Channel containing all FreeSurfer white matter parcellation files. Structure: [ val(meta), path(wmparc) ] | *.mgz |
| ch_aparc_aseg | file | Channel containing all FreeSurfer grey matter parcellation files. Structure: [ val(meta), path(aparc_aseg) ] | *.mgz |
| ch_dwi_bval_bvec | file | Channel containing all diffusion weighted images, b-values and b-vectors. Structure: [ val(meta), path(dwi), path(bval), path(bvec) ] | *.{nii.gz,bval,bvec} |
| ch_rev_dwi_bval_bvec | file | Channel containing all reverse encoded diffusion weighted images, b-values and b-vectors. Structure: [ val(meta), path(rev_dwi), path(rev_bval), path(rev_bvec) ] | *.{nii.gz,bval,bvec} |
| ch_rev_b0 | file | Channel containing all reverse b0 images. Structure: [ val(meta), path(rev_b0) ] | *.nii.gz |
| versions | file | File containing software versions Structure: [ path(versions.yml) ] | versions.yml |
Components
| io/readbids |
Keywords
| IO |
| BIDS |
| Files |
Authors
@gagnonanthony
Maintainers
@gagnonanthony