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2 changes: 1 addition & 1 deletion dev/.buildinfo
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# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: ea9cba626ef42c051e3ea60f81fcb445
config: 260e07dd1f774787c78be8eca66e450a
tags: 645f666f9bcd5a90fca523b33c5a78b7
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=====================================
05. BIDS conversion for group studies
=====================================
Here, we show how to do BIDS conversion for group studies.
We will use the
`EEG Motor Movement/Imagery Dataset <https://doi.org/10.13026/C28G6P>`_
available on the PhysioBank database.
We recommend that you go through the more basic BIDS conversion example before
checking out this group conversion example: :ref:`ex-convert-mne-sample`
"""
""" # noqa: E501 D205 D400

# Authors: The MNE-BIDS developers
# SPDX-License-Identifier: BSD-3-Clause
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"cell_type": "markdown",
"metadata": {},
"source": [
"\n# 05. BIDS conversion for group studies\nHere, we show how to do BIDS conversion for group studies.\nWe will use the\n[EEG Motor Movement/Imagery Dataset](https://doi.org/10.13026/C28G6P)\navailable on the PhysioBank database.\nWe recommend that you go through the more basic BIDS conversion example before\nchecking out this group conversion example: `ex-convert-mne-sample`\n"
"\n# 05. BIDS conversion for group studies\n\nHere, we show how to do BIDS conversion for group studies.\nWe will use the\n[EEG Motor Movement/Imagery Dataset](https://doi.org/10.13026/C28G6P)\navailable on the PhysioBank database.\nWe recommend that you go through the more basic BIDS conversion example before\nchecking out this group conversion example: `ex-convert-mne-sample`\n"
]
},
{
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You can use MNE-BIDS interactively inspect your MEG or (i)EEG data.
Problematic channels can be marked as "bad", for example if the connected
sensor produced mostly noise or no signal at all. Similarly, you can declare
sensor produced mostly noise - or no signal at all. Similarly, you can declare
channels as "good", should you discover they were incorrectly marked as bad.
Bad channel selection can also be performed non-interactively.
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for the :ref:`Python Command Line Interface <python_cli>`.
.. _BrainVision data format: https://www.brainproducts.com/support-resources/brainvision-core-data-format-1-0/
""" # noqa:E501
""" # noqa: E501 D205 D400

# Authors: The MNE-BIDS developers
# SPDX-License-Identifier: BSD-3-Clause
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BIDSPath is MNE-BIDS's working horse when it comes to file and folder
operations. Learn here how to use it.
"""
""" # noqa: D400

# Authors: The MNE-BIDS developers
# SPDX-License-Identifier: BSD-3-Clause
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In this tutorial, we show how ``read_raw_bids`` can be used to load and
inspect BIDS-formatted data.
"""
""" # noqa: D400

# Authors: The MNE-BIDS developers
# SPDX-License-Identifier: BSD-3-Clause
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.. _BIDS dataset_description.json definition: https://bids-specification.readthedocs.io/en/latest/modality-agnostic-files.html#dataset-description
.. _ds000248 dataset_description.json: https://github.com/sappelhoff/bids-examples/blob/master/ds000248/dataset_description.json
""" # noqa: D400 D205 E501
""" # noqa: D400 E501

# Authors: The MNE-BIDS developers
# SPDX-License-Identifier: BSD-3-Clause
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In this tutorial, we show how ``update_sidecar_json`` can be used to update and
modify BIDS-formatted data.
"""
""" # noqa: D205 D400

# Authors: The MNE-BIDS developers
# SPDX-License-Identifier: BSD-3-Clause
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4. Cite ``mne-bids``.
.. currentmodule:: mne_bids
""" # noqa: E501
""" # noqa: E501 D205 D400

# Authors: The MNE-BIDS developers
# SPDX-License-Identifier: BSD-3-Clause
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.. _appendix VIII: https://bids-specification.readthedocs.io/en/stable/appendices/coordinate-systems.html
.. _background on FreeSurfer: https://mne.tools/dev/auto_tutorials/source-modeling/plot_background_freesurfer_mne
.. _MNE-Python coordinate frames: https://mne.tools/dev/auto_tutorials/source-modeling/plot_source_alignment.html
""" # noqa: E501
""" # noqa: E501 D400

# Authors: The MNE-BIDS developers
# SPDX-License-Identifier: BSD-3-Clause
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.. note:: For this example you will need to install ``matplotlib`` and
``nilearn`` on top of your usual ``mne-bids`` installation.
"""
""" # noqa: E501 D205 D400

# Authors: The MNE-BIDS developers
# SPDX-License-Identifier: BSD-3-Clause
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You may automatically convert Raw objects to BIDS-compatible files with
``write_raw_bids``. This example is for manually creating files/folders.
"""
""" # noqa: E501 D205 D400

# Authors: The MNE-BIDS developers
# SPDX-License-Identifier: BSD-3-Clause
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.. _BrainVision format: https://www.brainproducts.com/support-resources/brainvision-core-data-format-1-0/
.. _CapTrak: https://www.fieldtriptoolbox.org/faq/coordsys/#details-of-the-captrak-coordinate-system
""" # noqa: E501
""" # noqa: E501 D205 D400

# Authors: The MNE-BIDS developers
# SPDX-License-Identifier: BSD-3-Clause
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"cell_type": "markdown",
"metadata": {},
"source": [
"\n# 03. Interactive data inspection and bad channel selection\n\nYou can use MNE-BIDS interactively inspect your MEG or (i)EEG data.\nProblematic channels can be marked as \"bad\", for example if the connected\nsensor produced mostly noise \u2013 or no signal at all. Similarly, you can declare\nchannels as \"good\", should you discover they were incorrectly marked as bad.\nBad channel selection can also be performed non-interactively.\n\nFurthermore, you can view and edit the experimental events and mark time\nsegments as \"bad\".\n\n"
"\n# 03. Interactive data inspection and bad channel selection\n\nYou can use MNE-BIDS interactively inspect your MEG or (i)EEG data.\nProblematic channels can be marked as \"bad\", for example if the connected\nsensor produced mostly noise - or no signal at all. Similarly, you can declare\nchannels as \"good\", should you discover they were incorrectly marked as bad.\nBad channel selection can also be performed non-interactively.\n\nFurthermore, you can view and edit the experimental events and mark time\nsegments as \"bad\".\n\n"
]
},
{
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This example demonstrates how to store empty room data "manually" in the BIDS
format and how to retrieve them.
"""
""" # noqa: E501 D400

# Authors: The MNE-BIDS developers
# SPDX-License-Identifier: BSD-3-Clause
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6 changes: 3 additions & 3 deletions dev/_modules/index.html
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Overview: module code &#8212; MNE-BIDS 0.16.0.dev17+g91655260 documentation</title>
<title>Overview: module code &#8212; MNE-BIDS 0.16.0.dev18+g1c9361cc documentation</title>



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<link rel="preload" as="script" href="../_static/scripts/pydata-sphinx-theme.js?digest=dfe6caa3a7d634c4db9b" />
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<script src="../_static/clipboard.min.js?v=a7894cd8"></script>
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<p class="title logo__title">MNE-BIDS 0.16.0.dev17+g91655260 documentation</p>
<p class="title logo__title">MNE-BIDS 0.16.0.dev18+g1c9361cc documentation</p>

</a></div>

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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>mne_bids.copyfiles &#8212; MNE-BIDS 0.16.0.dev17+g91655260 documentation</title>
<title>mne_bids.copyfiles &#8212; MNE-BIDS 0.16.0.dev18+g1c9361cc documentation</title>



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<link rel="preload" as="script" href="../../_static/scripts/pydata-sphinx-theme.js?digest=dfe6caa3a7d634c4db9b" />
<script src="../../_static/vendor/fontawesome/6.5.2/js/all.min.js?digest=dfe6caa3a7d634c4db9b"></script>

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<p class="title logo__title">MNE-BIDS 0.16.0.dev17+g91655260 documentation</p>
<p class="title logo__title">MNE-BIDS 0.16.0.dev18+g1c9361cc documentation</p>

</a></div>

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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>mne_bids.dig &#8212; MNE-BIDS 0.16.0.dev17+g91655260 documentation</title>
<title>mne_bids.dig &#8212; MNE-BIDS 0.16.0.dev18+g1c9361cc documentation</title>



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<link rel="preload" as="script" href="../../_static/scripts/pydata-sphinx-theme.js?digest=dfe6caa3a7d634c4db9b" />
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<p class="title logo__title">MNE-BIDS 0.16.0.dev17+g91655260 documentation</p>
<p class="title logo__title">MNE-BIDS 0.16.0.dev18+g1c9361cc documentation</p>

</a></div>

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6 changes: 3 additions & 3 deletions dev/_modules/mne_bids/inspect.html
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>mne_bids.inspect &#8212; MNE-BIDS 0.16.0.dev17+g91655260 documentation</title>
<title>mne_bids.inspect &#8212; MNE-BIDS 0.16.0.dev18+g1c9361cc documentation</title>



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<link rel="preload" as="script" href="../../_static/scripts/pydata-sphinx-theme.js?digest=dfe6caa3a7d634c4db9b" />
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<p class="title logo__title">MNE-BIDS 0.16.0.dev17+g91655260 documentation</p>
<p class="title logo__title">MNE-BIDS 0.16.0.dev18+g1c9361cc documentation</p>

</a></div>

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14 changes: 7 additions & 7 deletions dev/_modules/mne_bids/path.html
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>mne_bids.path &#8212; MNE-BIDS 0.16.0.dev17+g91655260 documentation</title>
<title>mne_bids.path &#8212; MNE-BIDS 0.16.0.dev18+g1c9361cc documentation</title>



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<link rel="preload" as="script" href="../../_static/scripts/pydata-sphinx-theme.js?digest=dfe6caa3a7d634c4db9b" />
<script src="../../_static/vendor/fontawesome/6.5.2/js/all.min.js?digest=dfe6caa3a7d634c4db9b"></script>

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<p class="title logo__title">MNE-BIDS 0.16.0.dev17+g91655260 documentation</p>
<p class="title logo__title">MNE-BIDS 0.16.0.dev18+g1c9361cc documentation</p>

</a></div>

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<span class="sd"> &quot;&quot;&quot;</span>
<span class="c1"># Take all possible data types from &quot;entity&quot; table</span>
<span class="c1"># (Appendix in BIDS spec)</span>
<span class="c1"># https://bids-specification.readthedocs.io/en/latest/appendices/entity-table.html # noqa</span>
<span class="c1"># https://bids-specification.readthedocs.io/en/latest/appendices/entity-table.html</span>
<span class="n">datatype_list</span> <span class="o">=</span> <span class="p">(</span><span class="s2">&quot;anat&quot;</span><span class="p">,</span> <span class="s2">&quot;func&quot;</span><span class="p">,</span> <span class="s2">&quot;dwi&quot;</span><span class="p">,</span> <span class="s2">&quot;fmap&quot;</span><span class="p">,</span> <span class="s2">&quot;beh&quot;</span><span class="p">,</span> <span class="s2">&quot;meg&quot;</span><span class="p">,</span> <span class="s2">&quot;eeg&quot;</span><span class="p">,</span> <span class="s2">&quot;ieeg&quot;</span><span class="p">,</span> <span class="s2">&quot;nirs&quot;</span><span class="p">)</span>
<span class="n">datatypes</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
<span class="k">for</span> <span class="n">root</span><span class="p">,</span> <span class="n">dirs</span><span class="p">,</span> <span class="n">files</span> <span class="ow">in</span> <span class="n">os</span><span class="o">.</span><span class="n">walk</span><span class="p">(</span><span class="n">root</span><span class="p">):</span>
<span class="k">for</span> <span class="nb">dir</span> <span class="ow">in</span> <span class="n">dirs</span><span class="p">:</span>
<span class="k">if</span> <span class="nb">dir</span> <span class="ow">in</span> <span class="n">datatype_list</span> <span class="ow">and</span> <span class="nb">dir</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">datatypes</span><span class="p">:</span>
<span class="n">datatypes</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">dir</span><span class="p">)</span>
<span class="k">for</span> <span class="n">_dir</span> <span class="ow">in</span> <span class="n">dirs</span><span class="p">:</span>
<span class="k">if</span> <span class="n">_dir</span> <span class="ow">in</span> <span class="n">datatype_list</span> <span class="ow">and</span> <span class="n">_dir</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">datatypes</span><span class="p">:</span>
<span class="n">datatypes</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">_dir</span><span class="p">)</span>

<span class="k">return</span> <span class="n">datatypes</span></div>

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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>mne_bids.read &#8212; MNE-BIDS 0.16.0.dev17+g91655260 documentation</title>
<title>mne_bids.read &#8212; MNE-BIDS 0.16.0.dev18+g1c9361cc documentation</title>



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<link rel="preload" as="script" href="../../_static/scripts/pydata-sphinx-theme.js?digest=dfe6caa3a7d634c4db9b" />
<script src="../../_static/vendor/fontawesome/6.5.2/js/all.min.js?digest=dfe6caa3a7d634c4db9b"></script>

<script src="../../_static/documentation_options.js?v=82d48278"></script>
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<p class="title logo__title">MNE-BIDS 0.16.0.dev17+g91655260 documentation</p>
<p class="title logo__title">MNE-BIDS 0.16.0.dev18+g1c9361cc documentation</p>

</a></div>

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<span class="k">if</span> <span class="n">updated_ch_type</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="c1"># XXX Try again with uppercase spelling – this should be removed</span>
<span class="c1"># XXX once https://github.com/bids-standard/bids-validator/issues/1018 # noqa:E501</span>
<span class="c1"># XXX once https://github.com/bids-standard/bids-validator/issues/1018</span>
<span class="c1"># XXX has been resolved.</span>
<span class="c1"># XXX x-ref https://github.com/mne-tools/mne-bids/issues/481</span>
<span class="n">updated_ch_type</span> <span class="o">=</span> <span class="n">bids_to_mne_ch_types</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">ch_type</span><span class="o">.</span><span class="n">upper</span><span class="p">(),</span> <span class="kc">None</span><span class="p">)</span>
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