Note
The following examples shown below correspond to the directory layouts shwon in the Usage section.
In the case of study directory layout 1, the command would look like:
$ study_proc \
--study-dir=</path/to/study/directory> \
--out-dir=</path/to/output/directory> \
--compress=6 \
--zero-pad=2 \
--append-dwi-info \
--verbose
Likewise, in python:
from convert_source.batch_convert import batch_proc
[imgs, jsons, bvals, bvecs] = batch_proc(study_img_dir='</path/to/study/directory>',
... out_dir='</path/to/output/directory>',
... append_dwi_info=True,
... zero_pad=2,
... cprss_lvl=6,
... verbose=True)
...
The corresponding output from both commands yeilds the follwing BIDS output directory:
Output_Directory
├── sub-001
| └── ses-001
| ├── anat
| | ├── sub-001_ses-001_run-01_T1w.json
| | └── sub-001_ses-001_run-01_T1w.nii.gz
| ├── dwi
| | ├── sub-001_ses-001_acq-TE88_run-01_sbref.json
| | ├── sub-001_ses-001_acq-TE88_run-01_sbref.nii.gz
| | ├── sub-001_ses-001_acq-b800b1500b2000TE88_run-01_dwi.bval
| | ├── sub-001_ses-001_acq-b800b1500b2000TE88_run-01_dwi.bvec
| | ├── sub-001_ses-001_acq-b800b1500b2000TE88_run-01_dwi.json
| | └── sub-001_ses-001_acq-b800b1500b2000TE88_run-01_dwi.nii.gz
| ├── func
| | ├── sub-001_ses-001_run-01_bold.json
| | ├── sub-001_ses-001_run-01_bold.nii.gz
| | ├── sub-001_ses-001_run-01_sbref.json
| | └── sub-001_ses-001_run-01_sbref.nii.gz
| └── fmap
| ├── sub-001_ses-001_run-01_magnitude.nii.gz
| ├── sub-001_ses-001_run-01_fieldmap.nii.gz
| └── sub-001_ses-001_run-01_fieldmap.json
├── sub-002
├── sub-003
├── sub-004
├── sub-005
├── sub-006
├── sub-007
├── sub-008
├── sub-009
├── sub-010
├── sub-011
├── sub-012
├── sub-013
├── sub-014
├── unknown
├──.bidsignore
└──.misc
Using the same commands from above on study directory layout 2, we get the following BIDS output directory layout:
Output_Directory
├── sub-001
| ├── anat
| | ├── sub-001_run-01_T1w.json
| | └── sub-001_run-01_T1w.nii.gz
| ├── dwi
| | ├── sub-001_acq-TE88_run-01_sbref.json
| | ├── sub-001_acq-TE88_run-01_sbref.nii.gz
| | ├── sub-001_acq-b800b1500b2000TE88_run-01_dwi.bval
| | ├── sub-001_acq-b800b1500b2000TE88_run-01_dwi.bvec
| | ├── sub-001_acq-b800b1500b2000TE88_run-01_dwi.json
| | └── sub-001_acq-b800b1500b2000TE88_run-01_dwi.nii.gz
| ├── func
| | ├── sub-001_run-01_bold.json
| | ├── sub-001_run-01_bold.nii.gz
| | ├── sub-001_run-01_sbref.json
| | └── sub-001_run-01_sbref.nii.gz
| └── fmap
| ├── sub-001_run-01_magnitude.nii.gz
| ├── sub-001_run-01_fieldmap.nii.gz
| └── sub-001_run-01_fieldmap.json
├── sub-002
├── sub-003
├── sub-004
├── sub-005
├── sub-006
├── sub-007
├── sub-008
├── sub-009
├── sub-010
├── sub-011
├── sub-012
├── sub-013
├── sub-014
├── unknown
├──.bidsignore
└──.misc
Likewise with study directory layout 3:
Output_Directory
├── sub-001
| ├── ses-001
| | ├── anat
| | | ├── sub-001_ses-001_run-01_T1w.json
| | | └── sub-001_ses-001_run-01_T1w.nii.gz
| | ├── dwi
| | | ├── sub-001_ses-001_acq-TE88_run-01_sbref.json
| | | ├── sub-001_ses-001_acq-TE88_run-01_sbref.nii.gz
| | | ├── sub-001_ses-001_acq-b800b1500b2000TE88_run-01_dwi.bval
| | | ├── sub-001_ses-001_acq-b800b1500b2000TE88_run-01_dwi.bvec
| | | ├── sub-001_ses-001_acq-b800b1500b2000TE88_run-01_dwi.json
| | | └── sub-001_ses-001_acq-b800b1500b2000TE88_run-01_dwi.nii.gz
| | ├── func
| | | ├── sub-001_ses-001_run-01_bold.json
| | | ├── sub-001_ses-001_run-01_bold.nii.gz
| | | ├── sub-001_ses-001_run-01_sbref.json
| | | └── sub-001_ses-001_run-01_sbref.nii.gz
| | └── fmap
| | ├── sub-001_ses-001_run-01_magnitude.nii.gz
| | ├── sub-001_ses-001_run-01_fieldmap.nii.gz
| | └── sub-001_ses-001_run-01_fieldmap.json
| └── ses-002
| ├── anat
| | ├── sub-001_ses-002_run-01_T1w.json
| | └── sub-001_ses-002_run-01_T1w.nii.gz
| ├── dwi
| | ├── sub-001_ses-002_acq-TE88_run-01_sbref.json
| | ├── sub-001_ses-002_acq-TE88_run-01_sbref.nii.gz
| | ├── sub-001_ses-002_acq-b800b1500b2000TE88_run-01_dwi.bval
| | ├── sub-001_ses-002_acq-b800b1500b2000TE88_run-01_dwi.bvec
| | ├── sub-001_ses-002_acq-b800b1500b2000TE88_run-01_dwi.json
| | └── sub-001_ses-002_acq-b800b1500b2000TE88_run-01_dwi.nii.gz
| ├── func
| | ├── sub-001_ses-002_run-01_bold.json
| | ├── sub-001_ses-002_run-01_bold.nii.gz
| | ├── sub-001_ses-002_run-01_sbref.json
| | └── sub-001_ses-002_run-01_sbref.nii.gz
| └── fmap
| ├── sub-001_ses-002_run-01_magnitude.nii.gz
| ├── sub-001_ses-002_run-01_fieldmap.nii.gz
| └── sub-001_ses-002_run-01_fieldmap.json
├── sub-002
├── sub-003
├── sub-004
├── sub-005
├── sub-006
├── sub-007
├── sub-008
├── sub-009
├── sub-010
├── sub-011
├── sub-012
├── sub-013
├── sub-014
├── unknown
├──.bidsignore
└──.misc