dcm2bids 2.1.2

Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure

|Documentation| |DOI|

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dcm2bids
========

``dcm2bids`` reorganises NIfTI files from
`dcm2niix <https://github.com/rordenlab/dcm2niix>`__ into the `Brain
Imaging Data Structure <http://bids.neuroimaging.io/>`__ (BIDS).

Before using this software, learn more about BIDS:

- read the BIDS
`specifications <https://bids-specification.readthedocs.io/en/stable/>`__
and the `paper <https://www.nature.com/articles/sdata201644>`__
- some dataset
`examples <https://github.com/bids-standard/bids-examples>`__

Follow the `guide <https://cbedetti.github.io/Dcm2Bids/guide>`__

Install
-------

``pip install dcm2bids``

or

``pip install --user dcm2bids``

Dependencies
------------

- `dcm2niix <https://github.com/rordenlab/dcm2niix>`__ to convert DICOM
to NIfTI. **You need to install it**

- `install
instructions <https://github.com/rordenlab/dcm2niix#install>`__
- `Recent
release <https://github.com/rordenlab/dcm2niix/releases>`__

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``
- Run the
`bids-validator <https://github.com/bids-standard/bids-validator>`__

dcm2bids creates log files inside
``<YOUR_FUTURE_BIDS_FOLDER>/tmp_dcm2bids/log``

Similar projects
----------------

Other tools to create `BIDS <http://bids.neuroimaging.io/>`__ datasets :

- `heudiconv <https://github.com/nipy/heudiconv>`__
- `bidskit <https://github.com/jmtyszka/bidskit>`__
- `dac2bids <https://github.com/dangom/dac2bids>`__

.. |Documentation| image:: https://img.shields.io/badge/documentation-read_it-succes.svg?logo=python
:target: https://cbedetti.github.io/Dcm2Bids
.. |DOI| image:: https://zenodo.org/badge/59581295.svg
:target: https://zenodo.org/badge/latestdoi/59581295