Metadata-Version: 1.2
Name: seek_localize
Version: 0.1.0
Summary: iEEG-BIDS anatomical and electrode coordinate interfacing software for easily generating anatomical interpretations of iEEG data.
Home-page: https://github.com/adam2302/seek_localize/
Author: ['Adam Li', 'Chester Huynh']
License: GNU General Public License (GPL)
Project-URL: Documentation, https://github.com/adam2302/seek_localize/doc/
Project-URL: Source, https://github.com/adam2302/seek_localize/
Project-URL: Tracker, https://github.com/adam2302/seek_localize/issues
Description: =======================================================
        seek_localize (Stereotactic ElectroEncephalography Kit)
        =======================================================
        
        .. image:: https://circleci.com/gh/adam2392/seek_localize.svg?style=svg
           :target: https://circleci.com/gh/adam2392/seek_localize
           :alt: CircleCI
        
        .. image:: https://github.com/adam2392/seek_localize/workflows/.github/workflows/main.yml/badge.svg
            :target: https://github.com/adam2392/seek_localize/actions/
            :alt: GitHub Actions
        
        .. image:: https://github.com/adam2392/seek_localize/workflows/test_suite/badge.svg
            :target: https://github.com/adam2392/seek_localize/workflows/test_suite/
            :alt: Test Suite
        
        .. image:: https://img.shields.io/badge/code%20style-black-000000.svg
           :target: https://github.com/ambv/black
           :alt: Code style: black
        
        .. image:: https://codecov.io/gh/adam2392/seek_localize/branch/master/graph/badge.svg
           :target: https://codecov.io/gh/adam2392/seek_localize
        
        .. image:: https://readthedocs.org/projects/seek_localize/badge/?version=latest
            :target: https://seek_localize.readthedocs.io/en/latest/?badge=latest
            :alt: Documentation Status
        
        .. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.4508674.svg
           :target: https://doi.org/10.5281/zenodo.4508674
        
        seek_localize helps localize iEEG electrodes on MRI/CT images and
        deals with data processing for iEEG-BIDS data.
        
        Documentation
        -------------
        The documentation can be found under the following links:
        
        - for the `stable release <https://seek_localize.readthedocs.io/en/stable/index.html>`_
        - for the `latest (development) version <https://seek_localize.readthedocs.io/en/latest/index.html>`_
        
        To see the ``seek`` documentation, see http://neuroseek.azurewebsites.net/docs/seek/
        
        
        Setup and Installation
        ----------------------
        
        See `INSTALLATION GUIDE <https://github.com/adam2392/seek_localize/blob/master/doc/installation.rst>`_ for full instructions.
        A quick setup can occur with github and ``pipenv``.
        
        .. code-block:: bash
        
            # clone repository locally
            $ git clone https://github.com/adam2392/seek_localize
            $ python3.8 -m venv .venv
            $ pipenv install
        
        Through pip
        
        .. code-block:: bash
        
            $ pip install seek_localize
        
        Quick Usage
        -----------
        Here is a quick look at a basic use-case, where we want to label the anatomical regions each
        electrode is in, based on FreeSurfer.
        
        .. code-block:: python
        
            from seek_localize import label_elecs_anat
            from mne_bids import BIDSPath
        
            # define file path to the T1w image that electrode coordinates are localized in
            img_fname = ...
        
            # define a path to the electrodes.tsv file in iEEG-BIDS
            bids_path = BIDSPath(..., suffix='electrodes', extension='.tsv')
        
            # define filepath to the FreeSurferColor Look up Table
            # (it is stored locally)
            fs_lut_fpath = seek_localize.fs_lut_fpath
        
            label_elecs_anat(bids_path, img_fname, fs_lut_fpath)
        
        
        Data Organization
        -----------------
        
        We use BIDS. See https://github.com/bids-standard/bids-starter-kit/wiki/The-BIDS-folder-hierarchy
        for more information. We recommend the following BIDS structure with the minimally required set of files.
        
        .. code-block::
        
           {bids_root}/
                /sub-001/
                    /anat/
                        - sub-001_*_T1w.nii
                    /ct/
                        - sub-001_*_CT.nii
                    /ieeg/
                        - sub-001_*_channels.tsv
                        - sub-001_*_electrodes.tsv
                        - *
        
        Development
        ===========
        seek_localize was created and is maintained by `Adam Li <https://adam2392.github.io>`_. It is also maintained and contributed by
        `Christopher Coogan <https://github.com/TheBrainChain>`_ and other researchers in the NCSL and Crone lab.
        Contributions are more than welcome so feel free to contact me, open an issue or submit a pull request! See the
        `contribution guide <https://github.com/adam2392/seek_localize/blob/master/docs/contributing.rst>`_.
        
        To report a bug, please visit the `GitHub repository <https://github.com/adam2392/seek_localize/issues/>`_.
        
        Note that this program is provided with NO WARRANTY OF ANY KIND. If you can, always double check the results with a
        human researcher, or clinician.
        
        How to cite?
        ============
        
        If you want to cite ``seek_localize``, please cite the following paper(s).
        
        Adam Li. (2021, February 5). seek_localize (Version 0.0.1). Zenodo. http://doi.org/10.5281/zenodo.4508674
        
        Acknowledgement
        ===============
        
        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., & Jas, M. (2019): **MNE-BIDS: Organizing
        electrophysiological data into the BIDS format and facilitating their analysis.**
        *Journal of Open Source Software,* 4:1896. DOI: [10.21105/joss.01896](https://doi.org/10.21105/joss.01896)
        
        
        FAQ
        ===
        1. For ECoG data, we do not explicitly have a process outlined, but these are significantly easier since grids can
        be easily interpolated. See `Fieldtrip Toolbox`_.
        
        .. _FieldTrip Toolbox: http://www.fieldtriptoolbox.org/tutorial/human_ecog/
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: Implementation
Classifier: Natural Language :: English
