Metadata-Version: 2.1
Name: dcm2bids
Version: 2.1.5
Summary: Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure
Home-page: UNKNOWN
Author: Christophe Bedetti
Author-email: christophe.bedetti@umontreal.ca
License: GPLv3+
Project-URL: Documentation, https://unfmontreal.github.io/Dcm2Bids
Project-URL: Source Code, https://github.com/unfmontreal/Dcm2Bids
Description: # dcm2bids
        
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        `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]
        
        ## Dependencies
        
        - [dcm2niix][dcm2niix-github] to convert DICOM to NIfTI. **You need to install it**
            - [install instructions][dcm2niix-install]
            - [Recent release][dcm2niix-release]
        
        ## Install
        
        `pip install dcm2bids`
        
        ## Upgrading
        
        `pip install --upgrade dcm2bids`
        
        ## TL;DR
        
        1. `mkdir <YOUR_FUTURE_BIDS_FOLDER>`
        2. `cd <YOUR_FUTURE_BIDS_FOLDER>`
        3. `dcm2bids_scaffold`
        4. `dcm2bids_helper -d <FOLDER_WITH_DICOMS_OF_A_TYPICAL_SESSION>`
        5. Build your configuration file with the help of the content of `tmp_dcm2bids/helper`
        6. `dcm2bids -d DICOM_DIR -p PARTICIPANT_ID -c CONFIG_FILE` for each participants of your study
        
        Follow the [tutorial](https://unfmontreal.github.io/Dcm2Bids/tutorial)
        
        dcm2bids creates log files inside `<YOUR_FUTURE_BIDS_FOLDER>/tmp_dcm2bids/log`
        
        ## bids-validator
        
        Run the [bids-validator][bids-validator] to check your directory. Don't forget to create a `.bidsignore` file at the root of your BIDS directory with `tmp_dcm2bids/*` inside.
        
        ## 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://unfmontreal.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
Classifier: Intended Audience :: Healthcare Industry
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: MacOS
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: Unix
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Requires-Python: >=3.5
Description-Content-Type: text/markdown
