Metadata-Version: 2.1
Name: dcm2bids
Version: 2.1.3
Summary: Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure
Home-page: https://github.com/cbedetti/Dcm2Bids
Author: Christophe Bedetti
Author-email: christophe.bedetti@umontreal.ca
License: UNKNOWN
Download-URL: https://github.com/cbedetti/Dcm2Bids/archive/2.1.3.tar.gz
Description: [![PyPI version](https://badge.fury.io/py/dcm2bids.svg)](https://pypi.org/project/dcm2bids) [![Documentation](https://img.shields.io/badge/documentation-dcm2bids-succes.svg)](https://cbedetti.github.io/Dcm2Bids) [![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.2616548.svg)](https://zenodo.org/badge/latestdoi/59581295)
        
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        # dcm2bids
        
        `dcm2bids` reorganises NIfTI files from [dcm2niix][dcm2niix-github] into the [Brain Imaging Data Structure][bids] (BIDS).
        
        Before using this software, learn more about BIDS:
        
        - read the BIDS [specifications][bids-spec] and the [paper][bids-nature]
        - some dataset [examples][bids-examples]
        
        Follow the [guide](https://cbedetti.github.io/Dcm2Bids/guide)
        
        ## Install
        
        `pip install dcm2bids`
        
        or
        
        `pip install --user dcm2bids`
        
        ## Dependencies
        
        - [dcm2niix][dcm2niix-github] to convert DICOM to NIfTI. **You need to install it**
            - [install instructions][dcm2niix-install]
            - [Recent release][dcm2niix-release]
        
        ## Upgrading
        
        `pip install --upgrade dcm2bids`
        
        # TL;DR
        
        Steps to get your data in BIDS :
        
        - `cd <YOUR_FUTURE_BIDS_FOLDER>`
        - `dcm2bids_scaffold`
        - `dcm2bids_helper -d <FOLDER_WITH_DICOMS_OF_A_TYPICAL_SESSION>`
        - Build your configuration file with the help of the content of `tmp_dcm2bids/helper`
        - `dcm2bids -d DICOM_DIR -p PARTICIPANT_ID -c CONFIG_FILE` for each participants of your study
        - Run the [bids-validator][bids-validator]
        
        dcm2bids creates log files inside `<YOUR_FUTURE_BIDS_FOLDER>/tmp_dcm2bids/log`
        
        ## Similar projects
        
        Other tools to create [BIDS][bids] datasets :
        
        - [heudiconv][link-heudiconv]
        - [bidskit][link-bidskit]
        - [dac2bids][link-dac2bids]
        
        [bids]: http://bids.neuroimaging.io/
        [bids-examples]: https://github.com/bids-standard/bids-examples
        [bids-nature]: https://www.nature.com/articles/sdata201644
        [bids-spec]: https://bids-specification.readthedocs.io/en/stable/
        [bids-validator]: https://github.com/bids-standard/bids-validator
        [dcm2bids-doc]: https://cbedetti.github.io/Dcm2Bids
        [dcm2niix-github]: https://github.com/rordenlab/dcm2niix
        [dcm2niix-install]: https://github.com/rordenlab/dcm2niix#install
        [dcm2niix-release]: https://github.com/rordenlab/dcm2niix/releases
        [link-heudiconv]: https://github.com/nipy/heudiconv
        [link-bidskit]: https://github.com/jmtyszka/bidskit
        [link-dac2bids]: https://github.com/dangom/dac2bids
        
Platform: UNKNOWN
Description-Content-Type: text/markdown
