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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: cd35824e6e3df82396b0759341f0acb0 | ||
config: f304eda2a80f76f9f9a22b252adbfb46 | ||
tags: 645f666f9bcd5a90fca523b33c5a78b7 |
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}, | ||
"outputs": [], | ||
"source": [ | ||
"# Authors: Adam Li <[email protected]>\n# Richard H\u00f6chenberger <[email protected]>\n# Alex Rockhill <[email protected]>\n#\n# License: BSD-3-Clause" | ||
"# Authors: The MNE-BIDS developers\n# SPDX-License-Identifier: BSD-3-Clause" | ||
] | ||
}, | ||
{ | ||
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}, | ||
"outputs": [], | ||
"source": [ | ||
"# Authors: Stefan Appelhoff <[email protected]>\n#\n# License: BSD-3-Clause" | ||
"# Authors: The MNE-BIDS developers\n# SPDX-License-Identifier: BSD-3-Clause" | ||
] | ||
}, | ||
{ | ||
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}, | ||
"outputs": [], | ||
"source": [ | ||
"# Authors: Richard H\u00f6chenberger <[email protected]>\n# Stefan Appelhoff <[email protected]>\n#\n# License: BSD-3-Clause" | ||
"# Authors: The MNE-BIDS developers\n# SPDX-License-Identifier: BSD-3-Clause" | ||
] | ||
}, | ||
{ | ||
|
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checking out this group conversion example: :ref:`ex-convert-mne-sample` | ||
""" | ||
|
||
# Authors: Mainak Jas <[email protected]> | ||
# Teon Brooks <[email protected]> | ||
# Stefan Appelhoff <[email protected]> | ||
# | ||
# License: BSD-3-Clause | ||
# Authors: The MNE-BIDS developers | ||
# SPDX-License-Identifier: BSD-3-Clause | ||
|
||
# %% | ||
# Let us import ``mne_bids`` | ||
|
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}, | ||
"outputs": [], | ||
"source": [ | ||
"# Authors: Mainak Jas <[email protected]>\n# Teon Brooks <[email protected]>\n# Stefan Appelhoff <[email protected]>\n#\n# License: BSD-3-Clause" | ||
"# Authors: The MNE-BIDS developers\n# SPDX-License-Identifier: BSD-3-Clause" | ||
] | ||
}, | ||
{ | ||
|
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.. _MNE-Python Annotations tutorial: https://mne.tools/stable/auto_tutorials/raw/30_annotate_raw.html#annotating-raw-objects-interactively | ||
""" # noqa: E501 D400 D205 | ||
|
||
# Authors: Richard Höchenberger <[email protected]> | ||
# | ||
# License: BSD-3-Clause | ||
# Authors: The MNE-BIDS developers | ||
# SPDX-License-Identifier: BSD-3-Clause | ||
|
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# %% | ||
# We will demonstrate how to mark individual channels as bad on the MNE | ||
|
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.. _BrainVision data format: https://www.brainproducts.com/support-resources/brainvision-core-data-format-1-0/ | ||
""" # noqa:E501 | ||
|
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# Authors: Stefan Appelhoff <[email protected]> | ||
# | ||
# License: BSD-3-Clause | ||
# Authors: The MNE-BIDS developers | ||
# SPDX-License-Identifier: BSD-3-Clause | ||
|
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# %% | ||
# We are importing everything we need for this example: | ||
|
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# For converting data files, or writing new data to the BrainVision format, you | ||
# can use :mod:`mne.export` or have a look at the `pybv`_ Python package. | ||
# | ||
# There is node JS tool to check the integrity of your BrainVision files. | ||
# For that, see the `BrainVision Validator <bv-validator_>`_ | ||
# | ||
# .. _`pybv`: https://github.com/bids-standard/pybv | ||
# .. _`bv-validator`: https://github.com/sappelhoff/brainvision-validator | ||
# | ||
# References | ||
# ---------- | ||
|
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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. | ||
""" | ||
# Authors: Richard Höchenberger <[email protected]> | ||
# Stefan Appelhoff <[email protected]> | ||
# | ||
# License: BSD-3-Clause | ||
|
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# Authors: The MNE-BIDS developers | ||
# SPDX-License-Identifier: BSD-3-Clause | ||
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# %% | ||
# Obviously, to start exploring BIDSPath, we first need to import it. | ||
|
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}, | ||
"outputs": [], | ||
"source": [ | ||
"# Authors: Mainak Jas <[email protected]>\n# Alexandre Gramfort <[email protected]>\n# Teon Brooks <[email protected]>\n# Stefan Appelhoff <[email protected]>\n# Richard H\u00f6chenberger <[email protected]>\n#\n# License: BSD-3-Clause" | ||
"# Authors: The MNE-BIDS developers\n# SPDX-License-Identifier: BSD-3-Clause" | ||
] | ||
}, | ||
{ | ||
|
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}, | ||
"outputs": [], | ||
"source": [ | ||
"# Authors: Mainak Jas <[email protected]>\n#\n# License: BSD-3-Clause" | ||
"# Authors: The MNE-BIDS developers\n# SPDX-License-Identifier: BSD-3-Clause" | ||
] | ||
}, | ||
{ | ||
|
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inspect BIDS-formatted data. | ||
""" | ||
# Authors: Adam Li <[email protected]> | ||
# Richard Höchenberger <[email protected]> | ||
# Alex Rockhill <[email protected]> | ||
# | ||
# License: BSD-3-Clause | ||
|
||
# Authors: The MNE-BIDS developers | ||
# SPDX-License-Identifier: BSD-3-Clause | ||
|
||
# %% | ||
# Imports | ||
|
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}, | ||
"outputs": [], | ||
"source": [ | ||
"# Authors: Adam Li <[email protected]>\n# mne-bids developers\n#\n# License: BSD-3-Clause" | ||
"# Authors: The MNE-BIDS developers\n# SPDX-License-Identifier: BSD-3-Clause" | ||
] | ||
}, | ||
{ | ||
|
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}, | ||
"outputs": [], | ||
"source": [ | ||
"# Authors: Richard H\u00f6chenberger <[email protected]>\n# License: BSD-3-Clause" | ||
"# Authors: The MNE-BIDS developers\n# SPDX-License-Identifier: BSD-3-Clause" | ||
] | ||
}, | ||
{ | ||
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@@ -26,7 +26,7 @@ | |
}, | ||
"outputs": [], | ||
"source": [ | ||
"import shutil\nfrom pathlib import Path\n\nimport mne\n\nfrom mne_bids import (\n BIDSPath,\n anonymize_dataset,\n print_dir_tree,\n write_anat,\n write_meg_calibration,\n write_meg_crosstalk,\n write_raw_bids,\n)\n\ndata_path = Path(mne.datasets.sample.data_path())\nevent_id = {\n \"Auditory/Left\": 1,\n \"Auditory/Right\": 2,\n \"Visual/Left\": 3,\n \"Visual/Right\": 4,\n \"Smiley\": 5,\n \"Button\": 32,\n}\n\nraw_path = data_path / \"MEG\" / \"sample\" / \"sample_audvis_raw.fif\"\nraw_er_path = data_path / \"MEG\" / \"sample\" / \"ernoise_raw.fif\" # empty-room\nevents_path = data_path / \"MEG\" / \"sample\" / \"sample_audvis_raw-eve.fif\"\ncal_path = data_path / \"SSS\" / \"sss_cal_mgh.dat\"\nct_path = data_path / \"SSS\" / \"ct_sparse_mgh.fif\"\nt1w_path = data_path / \"subjects\" / \"sample\" / \"mri\" / \"T1.mgz\"\n\nbids_root = data_path.parent / \"MNE-sample-data-bids\"\nbids_root_anon = data_path.parent / \"MNE-sample-data-bids-anon\"" | ||
"import shutil\n\nimport mne\n\nfrom mne_bids import (\n BIDSPath,\n anonymize_dataset,\n print_dir_tree,\n write_anat,\n write_meg_calibration,\n write_meg_crosstalk,\n write_raw_bids,\n)\n\ndata_path = mne.datasets.sample.data_path()\nevent_id = {\n \"Auditory/Left\": 1,\n \"Auditory/Right\": 2,\n \"Visual/Left\": 3,\n \"Visual/Right\": 4,\n \"Smiley\": 5,\n \"Button\": 32,\n}\n\nraw_path = data_path / \"MEG\" / \"sample\" / \"sample_audvis_raw.fif\"\nraw_er_path = data_path / \"MEG\" / \"sample\" / \"ernoise_raw.fif\" # empty-room\nevents_path = data_path / \"MEG\" / \"sample\" / \"sample_audvis_raw-eve.fif\"\ncal_path = data_path / \"SSS\" / \"sss_cal_mgh.dat\"\nct_path = data_path / \"SSS\" / \"ct_sparse_mgh.fif\"\nt1w_path = data_path / \"subjects\" / \"sample\" / \"mri\" / \"T1.mgz\"\n\nbids_root = data_path.parent / \"MNE-sample-data-bids\"\nbids_root_anon = data_path.parent / \"MNE-sample-data-bids-anon\"" | ||
] | ||
}, | ||
{ | ||
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dev/_downloads/6f1e7a639e0699d6164445b55e6c116d/auto_examples_jupyter.zip
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.. _ds000248 dataset_description.json: https://github.com/sappelhoff/bids-examples/blob/master/ds000248/dataset_description.json | ||
""" # noqa: D400 D205 E501 | ||
|
||
# Authors: Mainak Jas <[email protected]> | ||
# Alexandre Gramfort <[email protected]> | ||
# Teon Brooks <[email protected]> | ||
# Stefan Appelhoff <[email protected]> | ||
# Richard Höchenberger <[email protected]> | ||
# | ||
# License: BSD-3-Clause | ||
# Authors: The MNE-BIDS developers | ||
# SPDX-License-Identifier: BSD-3-Clause | ||
|
||
# %% | ||
# First we import some basic Python libraries, followed by MNE-Python and its | ||
|
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@@ -10,10 +10,9 @@ | |
In this tutorial, we show how ``update_sidecar_json`` can be used to update and | ||
modify BIDS-formatted data. | ||
""" | ||
# Authors: Adam Li <[email protected]> | ||
# mne-bids developers | ||
# | ||
# License: BSD-3-Clause | ||
|
||
# Authors: The MNE-BIDS developers | ||
# SPDX-License-Identifier: BSD-3-Clause | ||
|
||
# %% | ||
# Imports | ||
|
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}, | ||
"outputs": [], | ||
"source": [ | ||
"# Authors: Stefan Appelhoff <[email protected]>\n# Alex Rockhill <[email protected]>\n# Alex Gramfort <[email protected]>\n#\n# License: BSD-3-Clause" | ||
"# Authors: The MNE-BIDS developers\n# SPDX-License-Identifier: BSD-3-Clause" | ||
] | ||
}, | ||
{ | ||
|
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}, | ||
"outputs": [], | ||
"source": [ | ||
"# Authors: Chris Holdgraf <[email protected]>\n#\n# License: BSD-3-Clause" | ||
"# Authors: The MNE-BIDS developers\n# SPDX-License-Identifier: BSD-3-Clause" | ||
] | ||
}, | ||
{ | ||
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}, | ||
"outputs": [], | ||
"source": [ | ||
"from mne_bids import BIDSPath" | ||
"import shutil\n\nimport mne\n\nfrom mne_bids import BIDSPath" | ||
] | ||
}, | ||
{ | ||
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}, | ||
"outputs": [], | ||
"source": [ | ||
"bids_path = BIDSPath(\n subject=\"01\", session=\"mysession\", datatype=\"meg\", root=\"path/to/project\"\n).mkdir()\nprint(bids_path.directory)" | ||
"my_root = mne.datasets.sample.data_path() # replace with *your* root folder\nbids_path = BIDSPath(\n subject=\"mneBIDStest\", session=\"mysession\", datatype=\"meg\", root=my_root\n).mkdir()\nprint(bids_path.directory)\n\n# clean up\nshutil.rmtree(my_root / \"sub-mneBIDStest\")" | ||
] | ||
} | ||
], | ||
|
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@@ -18,9 +18,8 @@ | |
""" # noqa: E501 | ||
|
||
# Authors: Robert Luke <[email protected]> | ||
# | ||
# License: BSD-3-Clause | ||
# Authors: The MNE-BIDS developers | ||
# SPDX-License-Identifier: BSD-3-Clause | ||
|
||
# %% | ||
# We are importing everything we need for this example: | ||
|
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@@ -41,11 +41,8 @@ | |
""" # noqa: E501 | ||
|
||
# Authors: Adam Li <[email protected]> | ||
# Stefan Appelhoff <[email protected]> | ||
# Alex Rockhill <[email protected]> | ||
# | ||
# License: BSD-3-Clause | ||
# Authors: The MNE-BIDS developers | ||
# SPDX-License-Identifier: BSD-3-Clause | ||
|
||
# %% | ||
|
||
|
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@@ -28,11 +28,9 @@ | |
``nilearn`` on top of your usual ``mne-bids`` installation. | ||
""" | ||
# Authors: Stefan Appelhoff <[email protected]> | ||
# Alex Rockhill <[email protected]> | ||
# Alex Gramfort <[email protected]> | ||
# | ||
# License: BSD-3-Clause | ||
|
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# Authors: The MNE-BIDS developers | ||
# SPDX-License-Identifier: BSD-3-Clause | ||
|
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# %% | ||
# Let's import everything we need for this example: | ||
|
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@@ -13,13 +13,16 @@ | |
``write_raw_bids``. This example is for manually creating files/folders. | ||
""" | ||
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# Authors: Chris Holdgraf <[email protected]> | ||
# | ||
# License: BSD-3-Clause | ||
# Authors: The MNE-BIDS developers | ||
# SPDX-License-Identifier: BSD-3-Clause | ||
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# %% | ||
# First we will import the relevant functions | ||
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import shutil | ||
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import mne | ||
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from mne_bids import BIDSPath | ||
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# %% | ||
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@@ -49,7 +52,11 @@ | |
# | ||
# You can also use MNE-BIDS to create folder hierarchies. | ||
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my_root = mne.datasets.sample.data_path() # replace with *your* root folder | ||
bids_path = BIDSPath( | ||
subject="01", session="mysession", datatype="meg", root="path/to/project" | ||
subject="mneBIDStest", session="mysession", datatype="meg", root=my_root | ||
).mkdir() | ||
print(bids_path.directory) | ||
|
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# clean up | ||
shutil.rmtree(my_root / "sub-mneBIDStest") |
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@@ -15,7 +15,7 @@ | |
}, | ||
"outputs": [], | ||
"source": [ | ||
"# Authors: Robert Luke <[email protected]>\n#\n# License: BSD-3-Clause" | ||
"# Authors: The MNE-BIDS developers\n# SPDX-License-Identifier: BSD-3-Clause" | ||
] | ||
}, | ||
{ | ||
|
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@@ -22,9 +22,8 @@ | |
""" # noqa: E501 | ||
|
||
# Authors: Stefan Appelhoff <[email protected]> | ||
# | ||
# License: BSD-3-Clause | ||
# Authors: The MNE-BIDS developers | ||
# SPDX-License-Identifier: BSD-3-Clause | ||
|
||
# %% | ||
# We are importing everything we need for this example: | ||
|
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@@ -15,7 +15,7 @@ | |
}, | ||
"outputs": [], | ||
"source": [ | ||
"# Authors: Richard H\u00f6chenberger <[email protected]>\n#\n# License: BSD-3-Clause" | ||
"# Authors: The MNE-BIDS developers\n# SPDX-License-Identifier: BSD-3-Clause" | ||
] | ||
}, | ||
{ | ||
|
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|
@@ -15,7 +15,7 @@ | |
}, | ||
"outputs": [], | ||
"source": [ | ||
"# Authors: Adam Li <[email protected]>\n# Stefan Appelhoff <[email protected]>\n# Alex Rockhill <[email protected]>\n#\n# License: BSD-3-Clause" | ||
"# Authors: The MNE-BIDS developers\n# SPDX-License-Identifier: BSD-3-Clause" | ||
] | ||
}, | ||
{ | ||
|
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@@ -18,12 +18,11 @@ | |
to do the heavy lifting for you, automatically. | ||
""" # noqa: D400 D205 | ||
|
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# Authors: Richard Höchenberger <[email protected]> | ||
# License: BSD-3-Clause | ||
# Authors: The MNE-BIDS developers | ||
# SPDX-License-Identifier: BSD-3-Clause | ||
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# %% | ||
import shutil | ||
from pathlib import Path | ||
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import mne | ||
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@@ -37,7 +36,7 @@ | |
write_raw_bids, | ||
) | ||
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data_path = Path(mne.datasets.sample.data_path()) | ||
data_path = mne.datasets.sample.data_path() | ||
event_id = { | ||
"Auditory/Left": 1, | ||
"Auditory/Right": 2, | ||
|
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@@ -9,9 +9,8 @@ | |
format and how to retrieve them. | ||
""" | ||
|
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# Authors: Mainak Jas <[email protected]> | ||
# | ||
# License: BSD-3-Clause | ||
# Authors: The MNE-BIDS developers | ||
# SPDX-License-Identifier: BSD-3-Clause | ||
|
||
# %% | ||
# We are dealing with MEG data, which is often accompanied by so-called | ||
|
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|
@@ -15,7 +15,7 @@ | |
}, | ||
"outputs": [], | ||
"source": [ | ||
"# Authors: Stefan Appelhoff <[email protected]>\n#\n# License: BSD-3-Clause" | ||
"# Authors: The MNE-BIDS developers\n# SPDX-License-Identifier: BSD-3-Clause" | ||
] | ||
}, | ||
{ | ||
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@@ -76,7 +76,7 @@ | |
"cell_type": "markdown", | ||
"metadata": {}, | ||
"source": [ | ||
"## Further information\n\nFor converting data files, or writing new data to the BrainVision format, you\ncan use :mod:`mne.export` or have a look at the `pybv`_ Python package.\n\nThere is node JS tool to check the integrity of your BrainVision files.\nFor that, see the [BrainVision Validator](bv-validator_)\n\n\n## References\n.. [1] Pernet, C.R., Appelhoff, S., Gorgolewski, K.J. et al. EEG-BIDS, an\n extension to the brain imaging data structure for\n electroencephalography. Sci Data 6, 103 (2019).\n https://doi.org/10.1038/s41597-019-0104-8\n\n" | ||
"## Further information\n\nFor converting data files, or writing new data to the BrainVision format, you\ncan use :mod:`mne.export` or have a look at the `pybv`_ Python package.\n\n\n## References\n.. [1] Pernet, C.R., Appelhoff, S., Gorgolewski, K.J. et al. EEG-BIDS, an\n extension to the brain imaging data structure for\n electroencephalography. Sci Data 6, 103 (2019).\n https://doi.org/10.1038/s41597-019-0104-8\n\n" | ||
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