Mainak Jas
721 lines
19 KiB
ReStructuredText
721 lines
19 KiB
ReStructuredText
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.. _documentation:
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Documentation
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=============
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This is where you can learn about all the things you can do with MNE. It contains **background information** and **tutorials** for taking a deep-dive into the techniques that MNE-python covers. You'll find practical information on how to use these methods with your data, and in many cases some high-level concepts underlying these methods.
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There are also **examples**, which contain a short use-case to highlight MNE-functionality and provide inspiration for the many things you can do with this package. You can also find a gallery of these examples in the `examples gallery <auto_examples/index.html>`_.
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**See the links below for an introduction to MNE-python, or click one of the sections on this page to see more.**
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<h4 class="panel-title">
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<a data-toggle="collapse" href="#collapse_intro">Introduction to MNE and Python</a>
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</h4>
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</div>
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<div id="collapse_intro" class="panel-collapse collapse in">
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<div class="panel-body">
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**Getting started**
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.. toctree::
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:maxdepth: 1
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getting_started.rst
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advanced_setup.rst
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auto_tutorials/plot_python_intro.rst
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**MNE basics**
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.. toctree::
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:maxdepth: 1
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tutorials/philosophy.rst
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manual/cookbook.rst
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whats_new.rst
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python_reference.rst
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auto_examples/index.rst
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generated/commands.rst
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auto_tutorials/plot_configuration.rst
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cited.rst
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faq.rst
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**More help**
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- :ref:`Cite MNE <cite>`
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- `Mailing list <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis/>`_ for analysis talk
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- `GitHub issues <https://github.com/mne-tools/mne-python/issues/>`_ for
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requests and bug reports
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- `Gitter <https://gitter.im/mne-tools/mne-python>`_ to chat with devs
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<div class="panel-heading">
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<h4 class="panel-title">
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<a data-toggle="collapse" href="#collapse_data">Data structures and containers</a>
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</h4>
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</div>
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<div id="collapse_data" class="panel-collapse collapse">
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<div class="panel-body">
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.. toctree::
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:maxdepth: 1
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auto_tutorials/plot_object_raw.rst
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auto_tutorials/plot_object_epochs.rst
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auto_tutorials/plot_object_evoked.rst
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auto_tutorials/plot_info.rst
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<div class="panel-heading">
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<h4 class="panel-title">
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<a data-toggle="collapse" href="#collapse_io">Data I/O and datasets</a>
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</h4>
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</div>
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<div id="collapse_io" class="panel-collapse collapse">
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<div class="panel-body">
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**Getting your data into MNE**
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.. toctree::
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:maxdepth: 1
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manual/io.rst
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auto_tutorials/plot_creating_data_structures.rst
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auto_tutorials/plot_metadata_epochs.rst
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auto_tutorials/plot_modifying_data_inplace.rst
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auto_tutorials/plot_ecog.rst
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manual/memory.rst
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manual/migrating.rst
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<details class="example_details">
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<summary><strong>Examples</strong></summary>
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.. toctree::
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:maxdepth: 1
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auto_examples/io/plot_elekta_epochs.rst
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auto_examples/io/plot_objects_from_arrays.rst
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auto_examples/io/plot_read_and_write_raw_data.rst
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auto_examples/io/plot_read_epochs.rst
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auto_examples/io/plot_read_events.rst
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auto_examples/io/plot_read_evoked.rst
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auto_examples/io/plot_read_noise_covariance_matrix.rst
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.. raw:: html
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</details>
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**Working with public datasets**
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.. toctree::
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:maxdepth: 1
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manual/datasets_index.rst
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auto_tutorials/plot_brainstorm_auditory.rst
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auto_tutorials/plot_brainstorm_phantom_ctf.rst
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auto_tutorials/plot_brainstorm_phantom_elekta.rst
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auto_tutorials/plot_phantom_4DBTi.rst
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auto_examples/datasets/plot_brainstorm_data.rst
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auto_examples/datasets/plot_megsim_data.rst
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auto_examples/datasets/plot_megsim_data_single_trial.rst
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auto_examples/datasets/spm_faces_dataset.rst
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<h4 class="panel-title">
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<a id="preprocessing" class="anchor-doc"></a>
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<a data-toggle="collapse" href="#collapse_preprocessing">Preprocessing (filtering, SSP, ICA, Maxwell filtering, ...)</a>
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</h4>
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</div>
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<div id="collapse_preprocessing" class="panel-collapse collapse">
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**Background**
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.. toctree::
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:maxdepth: 1
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auto_tutorials/plot_background_filtering.rst
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manual/preprocessing/ssp.rst
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manual/preprocessing/ica.rst
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manual/preprocessing/maxwell.rst
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manual/channel_interpolation.rst
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**Preprocessing your data**
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.. toctree::
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:maxdepth: 1
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auto_tutorials/plot_artifacts_detection.rst
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auto_tutorials/plot_artifacts_correction_filtering.rst
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auto_tutorials/plot_artifacts_correction_rejection.rst
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auto_tutorials/plot_artifacts_correction_ssp.rst
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auto_tutorials/plot_artifacts_correction_ica.rst
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auto_tutorials/plot_artifacts_correction_maxwell_filtering.rst
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<summary><strong>Examples</strong></summary>
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:maxdepth: 1
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auto_examples/preprocessing/plot_define_target_events.rst
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auto_examples/preprocessing/plot_eog_artifact_histogram.rst
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auto_examples/preprocessing/plot_find_ecg_artifacts.rst
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auto_examples/preprocessing/plot_find_eog_artifacts.rst
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auto_examples/preprocessing/plot_head_positions.rst
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auto_examples/preprocessing/plot_ica_comparison.rst
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auto_examples/preprocessing/plot_interpolate_bad_channels.rst
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auto_examples/preprocessing/plot_movement_compensation.rst
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auto_examples/preprocessing/plot_rereference_eeg.rst
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auto_examples/preprocessing/plot_resample.rst
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auto_examples/preprocessing/plot_run_ica.rst
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auto_examples/preprocessing/plot_shift_evoked.rst
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auto_examples/preprocessing/plot_virtual_evoked.rst
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auto_examples/preprocessing/plot_xdawn_denoising.rst
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</details>
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<div class="panel-heading">
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<h4 class="panel-title">
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<a id="visualization" class="anchor-doc"></a>
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<a data-toggle="collapse" href="#collapse_visualization">Visualization</a>
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</h4>
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</div>
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<div id="collapse_visualization" class="panel-collapse collapse">
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.. toctree::
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:maxdepth: 1
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auto_tutorials/plot_visualize_raw.rst
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auto_tutorials/plot_visualize_epochs.rst
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auto_tutorials/plot_visualize_evoked.rst
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auto_tutorials/plot_whitened.rst
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tutorials/report.rst
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<details class="example_details">
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<summary><strong>Examples</strong></summary>
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.. toctree::
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auto_examples/visualization/make_report.rst
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auto_examples/visualization/plot_3d_to_2d.rst
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auto_examples/visualization/plot_channel_epochs_image.rst
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auto_examples/visualization/plot_eeg_on_scalp.rst
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auto_examples/visualization/plot_evoked_topomap.rst
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auto_examples/visualization/plot_evoked_whitening.rst
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auto_examples/visualization/plot_meg_sensors.rst
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auto_examples/visualization/plot_parcellation.rst
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auto_examples/visualization/plot_sensor_noise_level.rst
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auto_examples/visualization/plot_ssp_projs_sensitivity_map.rst
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auto_examples/visualization/plot_topo_compare_conditions.rst
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auto_examples/visualization/plot_topo_customized.rst
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auto_examples/visualization/plot_xhemi.rst
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<div class="panel panel-default">
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<h4 class="panel-title">
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<a id="time-freq" class="anchor-doc"></a>
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<a data-toggle="collapse" href="#collapse_tf">Time- and frequency-domain analyses</a>
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</h4>
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</div>
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<div id="collapse_tf" class="panel-collapse collapse">
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**Tutorials**
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.. toctree::
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:maxdepth: 1
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auto_tutorials/plot_introduction.rst
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auto_tutorials/plot_epoching_and_averaging.rst
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auto_tutorials/plot_eeg_erp.rst
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auto_tutorials/plot_sensors_time_frequency.rst
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manual/time_frequency.rst
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.. raw:: html
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<details class="example_details">
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<summary><strong>Examples</strong></summary>
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.. toctree::
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:maxdepth: 1
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auto_examples/time_frequency/plot_compute_raw_data_spectrum.rst
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auto_examples/time_frequency/plot_compute_source_psd_epochs.rst
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auto_examples/time_frequency/plot_source_label_time_frequency.rst
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auto_examples/time_frequency/plot_source_power_spectrum.rst
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auto_examples/time_frequency/plot_source_space_time_frequency.rst
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auto_examples/time_frequency/plot_temporal_whitening.rst
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auto_examples/time_frequency/plot_time_frequency_global_field_power.rst
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auto_examples/time_frequency/plot_time_frequency_simulated.rst
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auto_examples/time_frequency/plot_compute_csd.rst
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</details>
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</div>
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</div>
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<div class="panel panel-default">
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<div class="panel-heading">
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<h4 class="panel-title">
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<a id="source-analysis" class="anchor-doc"></a>
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<a data-toggle="collapse" href="#collapse_source">Source-level analysis</a>
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</h4>
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</div>
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<div id="collapse_source" class="panel-collapse collapse">
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<div class="panel-body">
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**Background**
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.. toctree::
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:maxdepth: 1
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manual/source_localization/forward.rst
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manual/source_localization/inverse.rst
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manual/source_localization/morph.rst
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**Getting data to source space**
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.. toctree::
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:maxdepth: 1
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auto_tutorials/plot_source_alignment.rst
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auto_tutorials/plot_forward.rst
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auto_tutorials/plot_compute_covariance.rst
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auto_tutorials/plot_mne_dspm_source_localization.rst
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auto_tutorials/plot_mne_solutions.rst
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auto_tutorials/plot_dipole_fit.rst
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auto_tutorials/plot_point_spread.rst
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auto_tutorials/plot_dipole_orientations.rst
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auto_tutorials/plot_dics.rst
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.. raw:: html
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<details class="example_details">
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<summary><strong>Forward examples</strong></summary>
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.. toctree::
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:maxdepth: 1
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auto_examples/forward/plot_decimate_head_surface.rst
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auto_examples/forward/plot_forward_sensitivity_maps.rst
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auto_examples/forward/plot_left_cerebellum_volume_source.rst
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auto_examples/forward/plot_source_space_morphing.rst
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.. raw:: html
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</details>
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.. raw:: html
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<details class="example_details">
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<summary><strong>Inverse examples</strong></summary>
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.. toctree::
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:maxdepth: 1
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auto_examples/inverse/plot_compute_mne_inverse_epochs_in_label.rst
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auto_examples/inverse/plot_compute_mne_inverse_raw_in_label.rst
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auto_examples/inverse/plot_compute_mne_inverse_volume.rst
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auto_examples/inverse/plot_covariance_whitening_dspm.rst
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auto_examples/inverse/plot_custom_inverse_solver.rst
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auto_examples/inverse/plot_dics_source_power.rst
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auto_examples/inverse/plot_gamma_map_inverse.rst
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auto_examples/inverse/plot_label_activation_from_stc.rst
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auto_examples/inverse/plot_label_from_stc.rst
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auto_examples/inverse/plot_label_source_activations.rst
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auto_examples/inverse/plot_lcmv_beamformer.rst
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auto_examples/inverse/plot_lcmv_beamformer_volume.rst
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auto_examples/inverse/plot_mixed_source_space_inverse.rst
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auto_examples/inverse/plot_mixed_norm_inverse.rst
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auto_examples/inverse/plot_mne_crosstalk_function.rst
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auto_examples/inverse/plot_mne_point_spread_function.rst
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auto_examples/inverse/plot_morph_data.rst
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auto_examples/inverse/plot_rap_music.rst
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auto_examples/inverse/plot_read_stc.rst
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auto_examples/inverse/plot_read_inverse.rst
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auto_examples/inverse/plot_read_source_space.rst
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auto_examples/inverse/plot_snr_estimate.rst
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auto_examples/inverse/plot_tf_dics.rst
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auto_examples/inverse/plot_tf_lcmv.rst
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auto_examples/inverse/plot_time_frequency_mixed_norm_inverse.rst
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auto_examples/inverse/plot_vector_mne_solution.rst
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.. raw:: html
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</details>
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.. raw:: html
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<details class="example_details">
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<summary><strong>Simulation examples</strong></summary>
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.. toctree::
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:maxdepth: 1
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auto_examples/simulation/plot_simulate_evoked_data.rst
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auto_examples/simulation/plot_simulate_raw_data.rst
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.. raw:: html
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</details>
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.. raw:: html
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</div>
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</div>
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</div>
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<div class="panel panel-default">
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<div class="panel-heading">
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<h4 class="panel-title">
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<a data-toggle="collapse" href="#collapse_statistics">Statistics</a>
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</h4>
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</div>
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<div id="collapse_statistics" class="panel-collapse collapse">
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<div class="panel-body">
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**Background**
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.. toctree::
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:maxdepth: 1
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auto_tutorials/plot_background_statistics.rst
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**Sensor Space**
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.. toctree::
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:maxdepth: 1
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auto_tutorials/plot_stats_spatio_temporal_cluster_sensors.rst
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auto_tutorials/plot_stats_cluster_1samp_test_time_frequency.rst
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auto_tutorials/plot_stats_cluster_time_frequency.rst
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auto_tutorials/plot_stats_cluster_erp.rst
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.. raw:: html
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<details class="example_details">
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<summary><strong>Examples</strong></summary>
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.. toctree::
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:maxdepth: 1
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auto_examples/stats/plot_fdr_stats_evoked.rst
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auto_examples/stats/plot_cluster_stats_evoked.rst
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auto_examples/stats/plot_sensor_permutation_test.rst
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auto_examples/stats/plot_sensor_regression.rst
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auto_examples/stats/plot_linear_regression_raw.rst
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.. raw:: html
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</details>
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**Source Space**
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.. toctree::
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:maxdepth: 1
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auto_tutorials/plot_stats_cluster_time_frequency_repeated_measures_anova.rst
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auto_tutorials/plot_stats_cluster_spatio_temporal_2samp.rst
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auto_tutorials/plot_stats_cluster_spatio_temporal_repeated_measures_anova.rst
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auto_tutorials/plot_stats_cluster_spatio_temporal.rst
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.. raw:: html
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</div>
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</div>
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</div>
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<div class="panel panel-default">
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<div class="panel-heading">
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<h4 class="panel-title">
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<a id="machine-learning" class="anchor-doc"></a>
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<a data-toggle="collapse" href="#collapse_ml">Machine learning (decoding, encoding, MVPA)</a>
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</h4>
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</div>
|
|
<div id="collapse_ml" class="panel-collapse collapse">
|
|
<div class="panel-body">
|
|
|
|
**Decoding**
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
manual/decoding.rst
|
|
auto_tutorials/plot_sensors_decoding.rst
|
|
|
|
.. raw:: html
|
|
|
|
<details class="example_details">
|
|
<summary><strong>Examples</strong></summary>
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
auto_examples/decoding/decoding_rsa.rst
|
|
auto_examples/decoding/plot_decoding_csp_eeg.rst
|
|
auto_examples/decoding/plot_decoding_csp_space.rst
|
|
auto_examples/decoding/plot_decoding_csp_timefreq.rst
|
|
auto_examples/decoding/plot_decoding_spatio_temporal_source.rst
|
|
auto_examples/decoding/plot_decoding_spoc_CMC.rst
|
|
auto_examples/decoding/plot_decoding_time_generalization_conditions.rst
|
|
auto_examples/decoding/plot_decoding_unsupervised_spatial_filter.rst
|
|
auto_examples/decoding/plot_decoding_xdawn_eeg.rst
|
|
auto_examples/decoding/plot_ems_filtering.rst
|
|
auto_examples/decoding/plot_linear_model_patterns.rst
|
|
|
|
.. raw:: html
|
|
|
|
</details>
|
|
|
|
**Encoding**
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
auto_tutorials/plot_receptive_field.rst
|
|
|
|
.. raw:: html
|
|
|
|
<details class="example_details">
|
|
<summary><strong>Examples</strong></summary>
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
auto_examples/decoding/plot_receptive_field_mtrf.rst
|
|
|
|
.. raw:: html
|
|
|
|
</details>
|
|
|
|
.. raw:: html
|
|
|
|
</div>
|
|
</div>
|
|
</div>
|
|
|
|
|
|
<div class="panel panel-default">
|
|
<div class="panel-heading">
|
|
<h4 class="panel-title">
|
|
<a id="connectivity" class="anchor-doc"></a>
|
|
<a data-toggle="collapse" href="#collapse_connectivity">Connectivity</a>
|
|
</h4>
|
|
</div>
|
|
<div id="collapse_connectivity" class="panel-collapse collapse">
|
|
<div class="panel-body">
|
|
|
|
**Examples**
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
auto_examples/connectivity/plot_cwt_sensor_connectivity.rst
|
|
auto_examples/connectivity/plot_mixed_source_space_connectivity.rst
|
|
auto_examples/connectivity/plot_mne_inverse_coherence_epochs.rst
|
|
auto_examples/connectivity/plot_mne_inverse_connectivity_spectrum.rst
|
|
auto_examples/connectivity/plot_mne_inverse_label_connectivity.rst
|
|
auto_examples/connectivity/plot_mne_inverse_psi_visual.rst
|
|
auto_examples/connectivity/plot_sensor_connectivity.rst
|
|
|
|
.. raw:: html
|
|
|
|
</div>
|
|
</div>
|
|
</div>
|
|
|
|
|
|
<div class="panel panel-default">
|
|
<div class="panel-heading">
|
|
<h4 class="panel-title">
|
|
<a data-toggle="collapse" href="#collapse_realtime">Realtime</a>
|
|
</h4>
|
|
</div>
|
|
<div id="collapse_realtime" class="panel-collapse collapse">
|
|
<div class="panel-body">
|
|
|
|
**Examples**
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
auto_examples/realtime/ftclient_rt_average.rst
|
|
auto_examples/realtime/ftclient_rt_compute_psd.rst
|
|
auto_examples/realtime/plot_compute_rt_average.rst
|
|
auto_examples/realtime/plot_compute_rt_decoder.rst
|
|
auto_examples/realtime/rt_feedback_client.rst
|
|
auto_examples/realtime/rt_feedback_server.rst
|
|
|
|
.. raw:: html
|
|
|
|
</div>
|
|
</div>
|
|
</div>
|
|
|
|
<div class="panel panel-default">
|
|
<div class="panel-heading">
|
|
<h4 class="panel-title">
|
|
<a data-toggle="collapse" href="#collapse_c">MNE-C and MNE-MATLAB</a>
|
|
</h4>
|
|
</div>
|
|
<div id="collapse_c" class="panel-collapse collapse">
|
|
<div class="panel-body">
|
|
|
|
**MNE-C**
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
tutorials/command_line.rst
|
|
manual/c_reference.rst
|
|
manual/gui/analyze.rst
|
|
manual/gui/browse.rst
|
|
manual/appendix/bem_model.rst
|
|
manual/appendix/c_misc.rst
|
|
manual/appendix/c_release_notes.rst
|
|
manual/appendix/c_EULA.rst
|
|
manual/appendix/martinos.rst
|
|
|
|
**MNE-MATLAB**
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
manual/matlab.rst
|
|
|
|
|
|
.. raw:: html
|
|
|
|
</div>
|
|
</div>
|
|
</div>
|
|
|
|
|
|
<div class="panel panel-default">
|
|
<div class="panel-heading">
|
|
<h4 class="panel-title">
|
|
<a data-toggle="collapse" href="#collapse_contributing">Contributing</a>
|
|
</h4>
|
|
</div>
|
|
|
|
<div id="collapse_contributing" class="panel-collapse collapse">
|
|
<div class="panel-body">
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
|
|
contributing.rst
|
|
configure_git.rst
|
|
customizing_git.rst
|
|
|
|
.. raw:: html
|
|
|
|
</div>
|
|
</div>
|
|
</div>
|
|
</div>
|