Examples¶
Note
The following examples shown below correspond to the directory layouts shwon in the Usage section.
Study Directory Layout 1¶
Command Line Interface¶
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
Python Module Interface¶
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
Study Directory Layout 2¶
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
Study Directory Layout 3¶
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