Metadata-Version: 2.1
Name: convert_source
Version: 0.2.0a12
Summary: Converts and organises source MR image data-sets in accordance with the Brain Imaging Data Structure (BIDS)
Home-page: https://github.com/AdebayoBraimah/convert_source
Author: Adebayo Braimah
Author-email: adebayo.braimah@gmail.com
License: GPL-3.0 License
Description: [![CircleCI](https://circleci.com/gh/AdebayoBraimah/convert_source.svg?style=svg)](https://app.circleci.com/pipelines/github/AdebayoBraimah/convert_source) [![Documentation Status](https://readthedocs.org/projects/convert-source/badge/?version=latest)](https://convert-source.readthedocs.io/en/latest/)
        
        # convert_source
        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:
                                False].
          --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.
        ```
        
Keywords: bids mri imaging neuroimaging dicom par rec nifti
Platform: UNKNOWN
Classifier: Intended Audience :: Science/Research
Classifier: Natural Language :: English
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3.7
Description-Content-Type: text/markdown
