Converts and organises source MR image data-sets in accordance with the Brain Imaging Data Structure (BIDS)

bids, mri, imaging, neuroimaging, dicom, par, rec, nifti, conversion, pet, data-sharing, data-standards, brain-imaging, parrec
pip install convert-source==0.2.0a12


CircleCI Documentation Status


Convert source DICOM, PAR REC or NIFTI image data to BIDS directory layout.

The YAML configuration file used as input dictates the search terms used to find and rename files. Please see config/config.default.yml or config/config.example.yml for examples.

Requires dcm2niix and pydicom.

usage: study_proc [-h] [-s STUDY_DIR] [-o OUT_DIR] [-c CONFIG.yml] [--no-gzip]
                  [--compress INT] [--zero-pad INT] [--append-dwi-info]
                  [--verbose] [--version] [--path-env PATH_VAR]

Convert source data of a study's imaging data to BIDS NIFTI data.

optional arguments:
  -h, --help            show this help message and exit

Required Argument(s):
  -s STUDY_DIR, -study STUDY_DIR, --study-dir STUDY_DIR
                        Parent study image directory for all subjects.
  -o OUT_DIR, -out OUT_DIR, --out-dir OUT_DIR
                        Output directory.

Optional Argument(s):
  -c CONFIG.yml, -config CONFIG.yml, --config-file CONFIG.yml
                        Input YAML configuration file. If no configuration
                        file is provided, then the default configuration file
                        is used.
  --no-gzip             DO NOT gzip the resulting BIDS NIFTI files [default:
  --compress INT        Compression level [1 - 9] - 1 is fastest, 9 is
                        smallest [default: 6].
  --zero-pad INT        The amount of zeropadding to pad the run numbers of
                        the BIDS NIFTI files (e.g. '--zero-pad=2' corresponds
                        to '01') [default: 2].
  --append-dwi-info     RECOMMENDED: Appends DWI acquisition information
                        (unique non-zero b-values, and TE, in msec.) to BIDS
                        acquisition filename of diffusion weighted image files
                        [default: False].
  --verbose             Enables verbose output to the command line.
  --version             Prints the version of 'convert_source', then exits.

Expert Option(s):
  --path-env PATH_VAR   Environmental path variable or variables for
                        dependencies (e.g. the path to 'dcm2niix'). NOTE: This
                        option is repeatable, and can thus be specified
                        multiple times.