doc updates [skip ci]

dev/.buildinfo

@@ -1,4 +1,4 @@
 # 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

dev/_downloads/07841a9269d1816a3add41f32d8a5ed2/read_bids_datasets.ipynb

@@ -15,7 +15,7 @@
       },
       "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"
       ]
     },
     {

dev/_downloads/0bc5481d861907f3ba86dd37d953b980/convert_eeg_to_bids.ipynb

@@ -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"
       ]
     },
     {

dev/_downloads/0c7e85abda2fce1fe2c484ad9f9aaa81/bidspath.ipynb

@@ -15,7 +15,7 @@
       },
       "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"
       ]
     },
     {

dev/_downloads/1eed244ec75de0e6a9392a728e24219b/convert_group_studies.py

@@ -10,11 +10,8 @@
 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``

dev/_downloads/241c30601b8e062b34a8b85829a39a45/convert_group_studies.ipynb

@@ -15,7 +15,7 @@
       },
       "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"
       ]
     },
     {

dev/_downloads/3556547a51e51e9556bdd40badb8d4c8/mark_bad_channels.py

@@ -15,9 +15,8 @@
 .. _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
 
 # %%
 # We will demonstrate how to mark individual channels as bad on the MNE

dev/_downloads/49d15d935de3a358386688419eb26d73/rename_brainvision_files.py

@@ -29,9 +29,8 @@
 .. _BrainVision data format: https://www.brainproducts.com/support-resources/brainvision-core-data-format-1-0/
 """  # 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:
@@ -89,11 +88,7 @@
 # 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
 # ----------

dev/_downloads/4b11a3ce6cfd9d8cf2b976f8386a2f8f/bidspath.py

@@ -8,10 +8,9 @@
 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
+
+# Authors: The MNE-BIDS developers
+# SPDX-License-Identifier: BSD-3-Clause
 
 # %%
 # Obviously, to start exploring BIDSPath, we first need to import it.

dev/_downloads/529f3230e5683b7676557bd33b2ea01b/convert_mne_sample.ipynb

@@ -15,7 +15,7 @@
       },
       "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"
       ]
     },
     {

dev/_downloads/58cece9c8037ffebaaad2703d5ce7839/convert_empty_room.ipynb

@@ -15,7 +15,7 @@
       },
       "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"
       ]
     },
     {

dev/_downloads/5eebd75ee4f8ffd30e34a83e87d0e28b/read_bids_datasets.py

@@ -24,11 +24,9 @@
 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

dev/_downloads/6a10915cde9ea548655ec1feef4a85d1/update_bids_datasets.ipynb

@@ -15,7 +15,7 @@
       },
       "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"
       ]
     },
     {

dev/_downloads/6a8efa177441ca0b84ef1b16e3806949/anonymize_dataset.ipynb

@@ -15,7 +15,7 @@
       },
       "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"
       ]
     },
     {
@@ -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\""
       ]
     },
     {

dev/_downloads/86851480108d4b249520df3993b0222b/convert_mne_sample.py

@@ -15,13 +15,8 @@
 .. _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

dev/_downloads/8a652dc37d1d38cf986f15eab46d0f7d/update_bids_datasets.py

@@ -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

dev/_downloads/9160181635ad137cb4a8a5779295596c/convert_mri_and_trans.ipynb

@@ -15,7 +15,7 @@
       },
       "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"
       ]
     },
     {

dev/_downloads/9cf968a426e81cc54e7ebab7dc9ef899/create_bids_folder.ipynb

@@ -15,7 +15,7 @@
       },
       "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"
       ]
     },
     {
@@ -33,7 +33,7 @@
       },
       "outputs": [],
       "source": [
-        "from mne_bids import BIDSPath"
+        "import shutil\n\nimport mne\n\nfrom mne_bids import BIDSPath"
       ]
     },
     {
@@ -87,7 +87,7 @@
       },
       "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\")"
       ]
     }
   ],

dev/_downloads/9e546b1b08e67ca7572c8e76f5992643/convert_nirs_to_bids.py

@@ -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:

dev/_downloads/a577037ece7a732b0607a269316e55b8/convert_ieeg_to_bids.py

@@ -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
 
 # %%
 

dev/_downloads/b143d969421db5e73a9339985e158e7a/convert_mri_and_trans.py

@@ -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
+
+# Authors: The MNE-BIDS developers
+# SPDX-License-Identifier: BSD-3-Clause
 
 # %%
 # Let's import everything we need for this example:

dev/_downloads/b637816c94a7cf4caf2ce4be824a809e/create_bids_folder.py

@@ -13,13 +13,16 @@
    ``write_raw_bids``. This example is for manually creating files/folders.
 """
 
-# Authors: Chris Holdgraf <[email protected]>
-#
-# License: BSD-3-Clause
+# Authors: The MNE-BIDS developers
+# SPDX-License-Identifier: BSD-3-Clause
 
 # %%
 # First we will import the relevant functions
 
+import shutil
+
+import mne
+
 from mne_bids import BIDSPath
 
 # %%
@@ -49,7 +52,11 @@
 #
 # You can also use MNE-BIDS to create folder hierarchies.
 
+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)
+
+# clean up
+shutil.rmtree(my_root / "sub-mneBIDStest")

dev/_downloads/b666106ea850b55fb6bc69db6fdda679/convert_nirs_to_bids.ipynb

@@ -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"
       ]
     },
     {

dev/_downloads/b7d549fc992398180d012ad4f3a73e8d/convert_eeg_to_bids.py

@@ -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:

dev/_downloads/bcdfe0d0e220cf6da56beb8f9163c326/mark_bad_channels.ipynb

@@ -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"
       ]
     },
     {

dev/_downloads/cf640e6bfa39f55978e620ef4269fd4c/convert_ieeg_to_bids.ipynb

@@ -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"
       ]
     },
     {

dev/_downloads/d5b79ff106a037057e89cb5616b1b839/anonymize_dataset.py

@@ -18,12 +18,11 @@
 to do the heavy lifting for you, automatically.
 """  # noqa: D400 D205
 
-# Authors: Richard Höchenberger <[email protected]>
-# License: BSD-3-Clause
+# Authors: The MNE-BIDS developers
+# SPDX-License-Identifier: BSD-3-Clause
 
 # %%
 import shutil
-from pathlib import Path
 
 import mne
 
@@ -37,7 +36,7 @@
     write_raw_bids,
 )
 
-data_path = Path(mne.datasets.sample.data_path())
+data_path = mne.datasets.sample.data_path()
 event_id = {
     "Auditory/Left": 1,
     "Auditory/Right": 2,

dev/_downloads/f336dfe6a8ab84474813b87342e0c0a3/convert_empty_room.py

@@ -9,9 +9,8 @@
 format and how to retrieve them.
 """
 
-# 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

dev/_downloads/fecfce9ee6664349717e6262ae61875d/rename_brainvision_files.ipynb

@@ -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"
       ]
     },
     {
@@ -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"
       ]
     }
   ],