Metadata-Version: 2.1
Name: mne-bids
Version: 0.4
Summary: MNE-BIDS: Organizing MEG, EEG, and iEEG data according to the BIDS specification and facilitating their analysis with MNE-Python
Home-page: https://mne.tools/mne-bids/
Maintainer: Mainak Jas
Maintainer-email: mainakjas@gmail.com
License: BSD (3-clause)
Download-URL: https://github.com/mne-tools/mne-bids.git
Project-URL: Documentation, https://mne.tools/mne-bids
Project-URL: Bug Reports, https://github.com/mne-tools/mne-bids/issues
Project-URL: Source, https://github.com/mne-tools/mne-bids
Description: 
        
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        MNE-BIDS
        ========
        
        This is a repository for creating
        `BIDS <https://bids.neuroimaging.io/>`_\ -compatible datasets with
        `MNE-Python <https://mne.tools/stable/index.html>`_.
        
        BIDS (Brain Imaging Data Structure) is a standard to organize data
        according to a set of rules that describe:
        
        - how to name your files
        - where to place your files within a directory structure
        - what additional metadata to store, and how to store it in sidecar json and tsv files
        
        The complete set of rules is written down in the
        `BIDS specification <https://bids-specification.readthedocs.io/en/stable/>`_.
        A BIDS-compatible dataset conforms to these rules and passes the
        `BIDS-validator <https://github.com/bids-standard/bids-validator>`_.
        
        MNE-Python is a software package for analyzing neurophysiology data.
        
        **MNE-BIDS links BIDS and MNE with the goal to make your analyses faster to code,
        more robust to errors, and easily shareable with colleagues.**
        
        Documentation
        -------------
        
        The documentation can be found under the following links:
        
        - for the `stable release <https://mne.tools/mne-bids/>`_
        - for the `latest (development) version <https://mne.tools/mne-bids/dev/index.html>`_
        
        Dependencies
        ------------
        
        * numpy (>=1.14)
        * scipy (>=0.18.1)
        * mne (>=0.19.1)
        * nibabel (>=2.2, optional)
        * pybv (optional)
        
        Installation
        ------------
        
        We recommend the `Anaconda <https://www.anaconda.com/download/>`_ Python
        distribution. We require that you use Python 3.5 or higher.
        You may choose to install ``mne-bids``
        `via pip <#Installation via pip>`_ or
        `via conda <#Installation via conda>`_.
        
        Installation via pip
        ####################
        
        Besides ``numpy`` and ``scipy`` (which are included in the standard Anaconda
        installation), you will need to install the most recent version of ``MNE``
        using the ``pip`` tool:
        
        .. code-block:: bash
        
           $ pip install -U mne
        
        
        Then install ``mne-bids``\ :
        
        .. code-block:: bash
        
           $ pip install -U mne-bids
        
        
        These ``pip`` commands also work if you want to upgrade if a newer version of
        ``mne-bids`` is available. If you do not have administrator privileges on the
        computer, use the ``--user`` flag with ``pip``.
        
        To check if everything worked fine, the following command should not give any
        error messages:
        
        .. code-block:: bash
        
           $ python -c 'import mne_bids'
        
        For full functionality of ``mne-bids``, you will also need to ``pip install``
        the following packages:
        
        - ``nibabel``, for interacting with MRI data
        - ``pybv``, to convert EEG data to BrainVision if input format is not valid according to EEG BIDS specifications
        
        If you want to use the latest development version of ``mne-bids``, use the
        following command:
        
        .. code-block:: bash
        
           $ pip install https://api.github.com/repos/mne-tools/mne-bids/zipball/master
        
        Installation via conda
        ######################
        
        If you have followed the
        `MNE-Python installation instructions <https://mne.tools/stable/install_mne_python.html#installing-mne-python-and-its-dependencies>`_,
        all that's left to do is to install ``mne-bids`` without its dependencies, as
        they've already been installed during the ``MNE`` installation process.
        
        Activate the correct ``conda`` environment and install ``mne-bids``:
        
        .. code-block:: bash
        
           $ conda activate mne
           $ conda install --channel conda-forge --no-deps mne-bids
        
        This approach ensures that the installation of ``mne-bids`` doesn't alter any
        other packages in your existing ``conda`` environment.
        
        Alternatively, you may wish to take advantage of the fact that the
        ``mne-bids`` package on ``conda-forge`` in fact depends on ``mne``,
        meaning that a "full" installation of ``mne-bids`` (i.e., including its
        dependencies) will provide you with a working copy of of both ``mne`` and
        ``mne-bids`` at once:
        
        .. code-block:: bash
        
           $ conda create --name mne --channel conda-forge mne-bids
        
        After activating the environment, you should be ready to use ``mne-bids``:
        
        .. code-block:: bash
        
           $ conda activate mne
           $ python -c 'import mne_bids'
        
        
        Quickstart
        ----------
        
        Currently, we support writing of BIDS datasets for MEG and EEG. Support for
        iEEG is experimental at the moment.
        
        .. code:: python
        
            >>> from mne import io
            >>> from mne_bids import write_raw_bids
            >>> raw = io.read_raw_fif('my_old_file.fif')
            >>> write_raw_bids(raw, 'sub-01_ses-01_run-05', bids_root='./bids_dataset')
        
        Command Line Interface
        ----------------------
        
        In addition to ``import mne_bids``, you can use the command line interface.
        Simply type ``mne_bids`` in your command line and press enter, to see the
        accepted commands. Then type ``mne_bids <command> --help``, where ``<command>``
        is one of the accepted commands, to get more information about that
        ``<command>``.
        
        Example:
        
        .. code-block:: bash
        
          $ mne_bids raw_to_bids --subject_id sub01 --task rest --raw data.edf --bids_root new_path
        
        Bug reports
        -----------
        
        Use the `GitHub issue tracker <https://github.com/mne-tools/mne-bids/issues>`_
        to report bugs.
        
        Contributing
        ------------
        
        Please see our `contributing guide <https://github.com/mne-tools/mne-bids/blob/master/CONTRIBUTING.md>`_.
        
        Cite
        ----
        
        If you use ``mne-bids`` in your work, please cite:
        
        .. code-block:: Text
        
            Appelhoff, S., Sanderson, M., Brooks, T., Vliet, M., Quentin, R., Holdgraf, C.,
            Chaumon, M., Mikulan, E., Tavabi, K., Höchenberger, R., Welke, D., Brunner, C.,
            Rockhill, A., Larson, E., Gramfort, A. and Jas, M. (2019). MNE-BIDS: Organizing
            electrophysiological data into the BIDS format and facilitating their analysis.
            Journal of Open Source Software 4: (1896).
        
        and one of the following papers, depending on which modality you used:
        
        `MEG <http://doi.org/10.1038/sdata.2018.110>`_
        ##############################################
        
        .. code-block:: Text
        
           Niso, G., Gorgolewski, K. J., Bock, E., Brooks, T. L., Flandin, G., Gramfort, A.,
           Henson, R. N., Jas, M., Litvak, V., Moreau, J., Oostenveld, R., Schoffelen, J.,
           Tadel, F., Wexler, J., Baillet, S. (2018). MEG-BIDS, the brain imaging data
           structure extended to magnetoencephalography. Scientific Data, 5, 180110.
           http://doi.org/10.1038/sdata.2018.110
        
        
        `EEG <https://doi.org/10.1038/s41597-019-0104-8>`_
        ##################################################
        
        .. code-block:: Text
        
           Pernet, C. R., Appelhoff, S., Gorgolewski, K. J., Flandin, G.,
           Phillips, C., Delorme, A., Oostenveld, R. (2019). EEG-BIDS, an extension
           to the brain imaging data structure for electroencephalography. Scientific
           Data, 6, 103. https://doi.org/10.1038/s41597-019-0104-8
        
        
        `iEEG <https://doi.org/10.1038/s41597-019-0105-7>`_
        ###################################################
        
        .. code-block:: Text
        
           Holdgraf, C., Appelhoff, S., Bickel, S., Bouchard, K., D'Ambrosio, S.,
           David, O., … Hermes, D. (2019). iEEG-BIDS, extending the Brain Imaging Data
           Structure specification to human intracranial electrophysiology. Scientific
           Data, 6, 102. https://doi.org/10.1038/s41597-019-0105-7
        
Platform: any
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved
Classifier: Programming Language :: Python
Classifier: Topic :: Software Development
Classifier: Topic :: Scientific/Engineering
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX
Classifier: Operating System :: Unix
Classifier: Operating System :: MacOS
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Requires-Python: ~=3.5
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