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