From 0c9fca5f1fb5068253bdefb6d4be32bafda18b98 Mon Sep 17 00:00:00 2001 From: Circle Ci Date: Thu, 7 Dec 2023 17:20:29 +0000 Subject: [PATCH] doc updates [skip ci] --- dev/.buildinfo | 2 +- .../read_bids_datasets.ipynb | 2 +- .../auto_examples_python.zip | Bin 101261 -> 100936 bytes .../convert_eeg_to_bids.ipynb | 4 +- .../convert_group_studies.py | 2 +- .../convert_group_studies.ipynb | 2 +- .../mark_bad_channels.py | 5 +- .../convert_mne_sample.ipynb | 6 +- .../convert_empty_room.ipynb | 2 +- .../read_bids_datasets.py | 9 +- .../update_bids_datasets.ipynb | 2 +- .../anonymize_dataset.ipynb | 2 +- .../auto_examples_jupyter.zip | Bin 155782 -> 155407 bytes .../convert_mne_sample.py | 18 +- .../update_bids_datasets.py | 4 +- .../convert_mri_and_trans.ipynb | 2 +- .../convert_nirs_to_bids.py | 4 +- .../convert_ieeg_to_bids.py | 49 +- .../convert_mri_and_trans.py | 12 +- .../convert_nirs_to_bids.ipynb | 4 +- .../convert_eeg_to_bids.py | 4 +- .../mark_bad_channels.ipynb | 2 +- .../convert_ieeg_to_bids.ipynb | 10 +- .../anonymize_dataset.py | 8 +- .../convert_empty_room.py | 3 +- dev/_modules/mne_bids/copyfiles.html | 20 +- dev/_modules/mne_bids/dig.html | 26 +- dev/_modules/mne_bids/inspect.html | 10 +- dev/_modules/mne_bids/path.html | 34 +- dev/_modules/mne_bids/read.html | 29 +- dev/_modules/mne_bids/report/_report.html | 17 +- dev/_modules/mne_bids/sidecar_updates.html | 14 +- dev/_modules/mne_bids/utils.html | 10 +- dev/_modules/mne_bids/write.html | 123 +- dev/auto_examples/anonymize_dataset.html | 70 +- dev/auto_examples/bidspath.html | 2 +- dev/auto_examples/convert_eeg_to_bids.html | 1059 +---------------- dev/auto_examples/convert_empty_room.html | 9 +- dev/auto_examples/convert_group_studies.html | 10 +- dev/auto_examples/convert_ieeg_to_bids.html | 240 +--- dev/auto_examples/convert_mne_sample.html | 24 +- dev/auto_examples/convert_mri_and_trans.html | 14 +- dev/auto_examples/convert_nirs_to_bids.html | 21 +- dev/auto_examples/mark_bad_channels.html | 7 +- dev/auto_examples/read_bids_datasets.html | 817 +------------ .../rename_brainvision_files.html | 2 +- dev/auto_examples/sg_execution_times.html | 48 +- dev/auto_examples/update_bids_datasets.html | 126 +- dev/searchindex.js | 2 +- dev/sg_execution_times.html | 48 +- 50 files changed, 404 insertions(+), 2536 deletions(-) diff --git a/dev/.buildinfo b/dev/.buildinfo index 4cfedd799..ac94bc8da 100644 --- a/dev/.buildinfo +++ b/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: cdc81cce15090a1726205caf1398f763 +config: a45f11a6cfb1de791052d41fb2dfb979 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/dev/_downloads/07841a9269d1816a3add41f32d8a5ed2/read_bids_datasets.ipynb b/dev/_downloads/07841a9269d1816a3add41f32d8a5ed2/read_bids_datasets.ipynb index 684edba0b..869fe8e04 100644 --- a/dev/_downloads/07841a9269d1816a3add41f32d8a5ed2/read_bids_datasets.ipynb +++ b/dev/_downloads/07841a9269d1816a3add41f32d8a5ed2/read_bids_datasets.ipynb @@ -33,7 +33,7 @@ }, "outputs": [], "source": [ - "import os\nimport os.path as op\nimport openneuro\n\nfrom mne.datasets import sample\nfrom mne_bids import (\n BIDSPath,\n read_raw_bids,\n print_dir_tree,\n make_report,\n find_matching_paths,\n get_entity_vals,\n)" + "import os\nimport os.path as op\n\nimport openneuro\nfrom mne.datasets import sample\n\nfrom mne_bids import (\n BIDSPath,\n find_matching_paths,\n get_entity_vals,\n make_report,\n print_dir_tree,\n read_raw_bids,\n)" ] }, { diff --git a/dev/_downloads/07fcc19ba03226cd3d83d4e40ec44385/auto_examples_python.zip b/dev/_downloads/07fcc19ba03226cd3d83d4e40ec44385/auto_examples_python.zip index 73ca295d9a44b722ec514133403485426dc4388a..495342e2bac52af6d09135377831d96dfd414085 100644 GIT binary patch delta 1863 zcmcgsZA@EL7{2dqQ?a8!X=!OG_EJ7dX~R-nh`@|4ZVMFC!Dg~4G_}xMDXzEmQcAQj zf{8*)5ZRfWVivO)Ke7akcrit%fn-KUm?l#bL$+k%mdt60oAKAOC7xT>*1Mtp^CqYF zr1!kfc|V@#nZk;*#}yS_oie$W5}#+20vawC8rzmmh@r`jXqE(-Dp?96esvao7 zZ@8hP#KDa4!6@tHeIwq!pnnLz9tS5X3HXISWHvQEZvqQ`qzueRH##qQG)Rr*h;aQ(QTZ7Q=+O1c05wM#l7iLooMWuv!-wyeIRV|bRRt))y1>NXV zG~JyP_?LCXr9J}JRTbBK)lE_2(o^`g1Q-Ni=6wa?SWW$%8o6Mfua7;-_=Xs=&8E){ zha%5s{)?bw%7$e!sK^vC{fQ36<}8@r38hHwG9tN4gPP||C@`l(Wu!ryDW&ky+>+T4 zupDIj!!ed;{Y-y2%=?3!FUqzuadh$7U^=ubr5n4YhgIpi#gcGM{iktp^eU$fcL#@4BJhN%)v1Z;@Pa_{5=KS>! 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If you are preparing a manuscript, please make sure to also # cite MNE-BIDS there. readme = op.join(output_path, "README") -with open(readme, "r", encoding="utf-8-sig") as fid: +with open(readme, encoding="utf-8-sig") as fid: text = fid.read() print(text) @@ -209,9 +209,7 @@ Alexandre Gramfort, Mainak Jas, and Stefan Appelhoff prepared and updated the \ data in BIDS format.""", data_license="CC0", - ethics_approvals=[ - "Human Subjects Division at the University of Washington" - ], # noqa: E501 + ethics_approvals=["Human Subjects Division at the University of Washington"], funding=[ "NIH 5R01EB009048", "NIH 1R01EB009048", @@ -234,7 +232,7 @@ overwrite=True, ) desc_json_path = bids_path.root / "dataset_description.json" -with open(desc_json_path, "r", encoding="utf-8-sig") as fid: +with open(desc_json_path, encoding="utf-8-sig") as fid: pprint(json.loads(fid.read())) # %% diff --git a/dev/_downloads/8a652dc37d1d38cf986f15eab46d0f7d/update_bids_datasets.py b/dev/_downloads/8a652dc37d1d38cf986f15eab46d0f7d/update_bids_datasets.py index 6b0ae077d..667e721c3 100644 --- a/dev/_downloads/8a652dc37d1d38cf986f15eab46d0f7d/update_bids_datasets.py +++ b/dev/_downloads/8a652dc37d1d38cf986f15eab46d0f7d/update_bids_datasets.py @@ -22,10 +22,10 @@ from mne.datasets import somato from mne_bids import ( - read_raw_bids, find_matching_paths, - print_dir_tree, make_report, + print_dir_tree, + read_raw_bids, update_sidecar_json, ) diff --git a/dev/_downloads/9160181635ad137cb4a8a5779295596c/convert_mri_and_trans.ipynb b/dev/_downloads/9160181635ad137cb4a8a5779295596c/convert_mri_and_trans.ipynb index 39ecbee66..09661b906 100644 --- a/dev/_downloads/9160181635ad137cb4a8a5779295596c/convert_mri_and_trans.ipynb +++ b/dev/_downloads/9160181635ad137cb4a8a5779295596c/convert_mri_and_trans.ipynb @@ -33,7 +33,7 @@ }, "outputs": [], "source": [ - "import os.path as op\nimport shutil\n\nimport numpy as np\nimport matplotlib.pyplot as plt\n\nfrom nilearn.plotting import plot_anat\n\nimport mne\nfrom mne.datasets import sample\nfrom mne import head_to_mri\n\nfrom mne_bids import (\n write_raw_bids,\n BIDSPath,\n write_anat,\n get_anat_landmarks,\n get_head_mri_trans,\n print_dir_tree,\n)" + "import os.path as op\nimport shutil\n\nimport matplotlib.pyplot as plt\nimport mne\nimport numpy as np\nfrom mne import head_to_mri\nfrom mne.datasets import sample\nfrom nilearn.plotting import plot_anat\n\nfrom mne_bids import (\n BIDSPath,\n get_anat_landmarks,\n get_head_mri_trans,\n print_dir_tree,\n write_anat,\n write_raw_bids,\n)" ] }, { diff --git a/dev/_downloads/9e546b1b08e67ca7572c8e76f5992643/convert_nirs_to_bids.py b/dev/_downloads/9e546b1b08e67ca7572c8e76f5992643/convert_nirs_to_bids.py index 2b80e5c5c..a18aa6f3f 100644 --- a/dev/_downloads/9e546b1b08e67ca7572c8e76f5992643/convert_nirs_to_bids.py +++ b/dev/_downloads/9e546b1b08e67ca7572c8e76f5992643/convert_nirs_to_bids.py @@ -31,7 +31,7 @@ import mne from mne_nirs import datasets # For convenient downloading of example data -from mne_bids import write_raw_bids, BIDSPath, print_dir_tree +from mne_bids import BIDSPath, print_dir_tree, write_raw_bids from mne_bids.stats import count_events # %% @@ -172,7 +172,7 @@ # If you are preparing a manuscript, please make sure to also cite MNE-BIDS # there. readme = op.join(bids_root, "README") -with open(readme, "r", encoding="utf-8-sig") as fid: +with open(readme, encoding="utf-8-sig") as fid: text = fid.read() print(text) diff --git a/dev/_downloads/a577037ece7a732b0607a269316e55b8/convert_ieeg_to_bids.py b/dev/_downloads/a577037ece7a732b0607a269316e55b8/convert_ieeg_to_bids.py index 659dbd886..bf0cf5a2b 100644 --- a/dev/_downloads/a577037ece7a732b0607a269316e55b8/convert_ieeg_to_bids.py +++ b/dev/_downloads/a577037ece7a732b0607a269316e55b8/convert_ieeg_to_bids.py @@ -50,24 +50,24 @@ # %% import os.path as op -import numpy as np import shutil +import mne import nibabel as nib +import numpy as np from nilearn.plotting import plot_anat -import mne from mne_bids import ( BIDSPath, - write_raw_bids, - write_anat, + convert_montage_to_mri, + convert_montage_to_ras, get_anat_landmarks, + print_dir_tree, read_raw_bids, search_folder_for_text, - print_dir_tree, template_to_head, - convert_montage_to_ras, - convert_montage_to_mri, + write_anat, + write_raw_bids, ) # %% @@ -289,11 +289,8 @@ # compare with standard print( - "Recovered coordinate: {recovered}\n" - "Saved coordinate: {saved}".format( - recovered=montage2.get_positions()["ch_pos"]["LENT 1"], - saved=montage.get_positions()["ch_pos"]["LENT 1"], - ) + f"Recovered coordinate: {montage2.get_positions()['ch_pos']['LENT 1']}\n" + f"Saved coordinate: {montage.get_positions()['ch_pos']['LENT 1']}" ) # %% @@ -303,7 +300,7 @@ # If you are preparing a manuscript, please make sure to also cite MNE-BIDS # there. readme = op.join(bids_root, "README") -with open(readme, "r", encoding="utf-8-sig") as fid: +with open(readme, encoding="utf-8-sig") as fid: text = fid.read() print(text) @@ -397,13 +394,11 @@ # check difference in trans print( - "Recovered trans:\n{recovered}\n" - "Original trans:\n{original}".format( - recovered=trans2["trans"].round(3), - # combine head->mri with mri->mni to get head->mni - # and then invert to get mni->head - original=np.linalg.inv(np.dot(trans["trans"], mri_mni_t["trans"])).round(3), - ) + f"Recovered trans:\n{trans2['trans'].round(3)}\n" + # combine head->mri with mri->mni to get head->mni + # and then invert to get mni->head + "Original trans:\n" + f"{np.linalg.inv(np.dot(trans['trans'], mri_mni_t['trans'])).round(3)}" ) # ensure that the data in MNI coordinates is exactly the same @@ -411,11 +406,8 @@ montage2 = raw2.get_montage() # get montage after transformed back to head montage2.apply_trans(trans2) print( - "Recovered coordinate: {recovered}\n" - "Original coordinate: {original}".format( - recovered=montage2.get_positions()["ch_pos"]["LENT 1"], - original=montage.get_positions()["ch_pos"]["LENT 1"], - ) + f"Recovered coordinate: {montage2.get_positions()['ch_pos']['LENT 1']}\n" + f"Original coordinate: {montage.get_positions()['ch_pos']['LENT 1']}" ) # %% @@ -521,11 +513,8 @@ montage2 = raw2.get_montage() # get montage after transformed back to head montage2.apply_trans(trans2) # apply trans to go back to 'mri' print( - "Recovered coordinate: {recovered}\n" - "Original coordinate: {original}".format( - recovered=montage2.get_positions()["ch_pos"]["LENT 1"], - original=montage.get_positions()["ch_pos"]["LENT 1"], - ) + f"Recovered coordinate: {montage2.get_positions()['ch_pos']['LENT 1']}\n" + f"Original coordinate: {montage.get_positions()['ch_pos']['LENT 1']}" ) # %% diff --git a/dev/_downloads/b143d969421db5e73a9339985e158e7a/convert_mri_and_trans.py b/dev/_downloads/b143d969421db5e73a9339985e158e7a/convert_mri_and_trans.py index a6a0e1310..cef828146 100644 --- a/dev/_downloads/b143d969421db5e73a9339985e158e7a/convert_mri_and_trans.py +++ b/dev/_downloads/b143d969421db5e73a9339985e158e7a/convert_mri_and_trans.py @@ -40,22 +40,20 @@ import os.path as op import shutil -import numpy as np import matplotlib.pyplot as plt - -from nilearn.plotting import plot_anat - import mne -from mne.datasets import sample +import numpy as np from mne import head_to_mri +from mne.datasets import sample +from nilearn.plotting import plot_anat from mne_bids import ( - write_raw_bids, BIDSPath, - write_anat, get_anat_landmarks, get_head_mri_trans, print_dir_tree, + write_anat, + write_raw_bids, ) # %% diff --git a/dev/_downloads/b666106ea850b55fb6bc69db6fdda679/convert_nirs_to_bids.ipynb b/dev/_downloads/b666106ea850b55fb6bc69db6fdda679/convert_nirs_to_bids.ipynb index 409472771..f175c9d7f 100644 --- a/dev/_downloads/b666106ea850b55fb6bc69db6fdda679/convert_nirs_to_bids.ipynb +++ b/dev/_downloads/b666106ea850b55fb6bc69db6fdda679/convert_nirs_to_bids.ipynb @@ -33,7 +33,7 @@ }, "outputs": [], "source": [ - "import os.path as op\nimport pathlib\nimport shutil\n\nimport mne\nfrom mne_nirs import datasets # For convenient downloading of example data\n\nfrom mne_bids import write_raw_bids, BIDSPath, print_dir_tree\nfrom mne_bids.stats import count_events" + "import os.path as op\nimport pathlib\nimport shutil\n\nimport mne\nfrom mne_nirs import datasets # For convenient downloading of example data\n\nfrom mne_bids import BIDSPath, print_dir_tree, write_raw_bids\nfrom mne_bids.stats import count_events" ] }, { @@ -231,7 +231,7 @@ }, "outputs": [], "source": [ - "readme = op.join(bids_root, \"README\")\nwith open(readme, \"r\", encoding=\"utf-8-sig\") as fid:\n text = fid.read()\nprint(text)" + "readme = op.join(bids_root, \"README\")\nwith open(readme, encoding=\"utf-8-sig\") as fid:\n text = fid.read()\nprint(text)" ] }, { diff --git a/dev/_downloads/b7d549fc992398180d012ad4f3a73e8d/convert_eeg_to_bids.py b/dev/_downloads/b7d549fc992398180d012ad4f3a73e8d/convert_eeg_to_bids.py index 54019b3eb..c207a3a7a 100644 --- a/dev/_downloads/b7d549fc992398180d012ad4f3a73e8d/convert_eeg_to_bids.py +++ b/dev/_downloads/b7d549fc992398180d012ad4f3a73e8d/convert_eeg_to_bids.py @@ -34,7 +34,7 @@ import mne from mne.datasets import eegbci -from mne_bids import write_raw_bids, BIDSPath, print_dir_tree +from mne_bids import BIDSPath, print_dir_tree, write_raw_bids from mne_bids.stats import count_events # %% @@ -221,7 +221,7 @@ # If you are preparing a manuscript, please make sure to also cite MNE-BIDS # there. readme = op.join(bids_root, "README") -with open(readme, "r", encoding="utf-8-sig") as fid: +with open(readme, encoding="utf-8-sig") as fid: text = fid.read() print(text) diff --git a/dev/_downloads/bcdfe0d0e220cf6da56beb8f9163c326/mark_bad_channels.ipynb b/dev/_downloads/bcdfe0d0e220cf6da56beb8f9163c326/mark_bad_channels.ipynb index e8376ec87..e0c619401 100644 --- a/dev/_downloads/bcdfe0d0e220cf6da56beb8f9163c326/mark_bad_channels.ipynb +++ b/dev/_downloads/bcdfe0d0e220cf6da56beb8f9163c326/mark_bad_channels.ipynb @@ -33,7 +33,7 @@ }, "outputs": [], "source": [ - "import os.path as op\nimport shutil\n\nimport mne\nfrom mne_bids import (\n BIDSPath,\n write_raw_bids,\n read_raw_bids,\n inspect_dataset,\n mark_channels,\n)\n\ndata_path = mne.datasets.sample.data_path()\nraw_fname = op.join(data_path, \"MEG\", \"sample\", \"sample_audvis_raw.fif\")\nevents_fname = op.join(data_path, \"MEG\", \"sample\", \"sample_audvis_raw-eve.fif\")\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}\nbids_root = op.join(data_path, \"..\", \"MNE-sample-data-bids\")\nbids_path = BIDSPath(\n subject=\"01\", session=\"01\", task=\"audiovisual\", run=\"01\", root=bids_root\n)" + "import os.path as op\nimport shutil\n\nimport mne\n\nfrom mne_bids import (\n BIDSPath,\n inspect_dataset,\n mark_channels,\n read_raw_bids,\n write_raw_bids,\n)\n\ndata_path = mne.datasets.sample.data_path()\nraw_fname = op.join(data_path, \"MEG\", \"sample\", \"sample_audvis_raw.fif\")\nevents_fname = op.join(data_path, \"MEG\", \"sample\", \"sample_audvis_raw-eve.fif\")\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}\nbids_root = op.join(data_path, \"..\", \"MNE-sample-data-bids\")\nbids_path = BIDSPath(\n subject=\"01\", session=\"01\", task=\"audiovisual\", run=\"01\", root=bids_root\n)" ] }, { diff --git a/dev/_downloads/cf640e6bfa39f55978e620ef4269fd4c/convert_ieeg_to_bids.ipynb b/dev/_downloads/cf640e6bfa39f55978e620ef4269fd4c/convert_ieeg_to_bids.ipynb index 952b1d772..0e62348c9 100644 --- a/dev/_downloads/cf640e6bfa39f55978e620ef4269fd4c/convert_ieeg_to_bids.ipynb +++ b/dev/_downloads/cf640e6bfa39f55978e620ef4269fd4c/convert_ieeg_to_bids.ipynb @@ -26,7 +26,7 @@ }, "outputs": [], "source": [ - "import os.path as op\nimport numpy as np\nimport shutil\n\nimport nibabel as nib\nfrom nilearn.plotting import plot_anat\n\nimport mne\nfrom mne_bids import (\n BIDSPath,\n write_raw_bids,\n write_anat,\n get_anat_landmarks,\n read_raw_bids,\n search_folder_for_text,\n print_dir_tree,\n template_to_head,\n convert_montage_to_ras,\n convert_montage_to_mri,\n)" + "import os.path as op\nimport shutil\n\nimport mne\nimport nibabel as nib\nimport numpy as np\nfrom nilearn.plotting import plot_anat\n\nfrom mne_bids import (\n BIDSPath,\n convert_montage_to_mri,\n convert_montage_to_ras,\n get_anat_landmarks,\n print_dir_tree,\n read_raw_bids,\n search_folder_for_text,\n template_to_head,\n write_anat,\n write_raw_bids,\n)" ] }, { @@ -213,7 +213,7 @@ }, "outputs": [], "source": [ - "montage2 = raw2.get_montage()\n\n# we need to go from scanner RAS back to surface RAS (requires recon-all)\nconvert_montage_to_mri(montage2, \"sample_seeg\", subjects_dir=subjects_dir)\n\n# this uses Freesurfer recon-all subject directory\nmontage2.add_estimated_fiducials(\"sample_seeg\", subjects_dir=subjects_dir)\n\n# get head->mri trans, invert from mri->head\ntrans2 = mne.transforms.invert_transform(mne.channels.compute_native_head_t(montage2))\n\n# now the montage is properly in \"head\" and ready for analysis in MNE\nraw2.set_montage(montage2)\n\n# get the monage, apply the trans and make sure it's the same\n# note: the head coordinates may differ because they are defined by\n# the fiducials which are estimated; as long as the head->mri trans\n# is computed with the same fiducials, the coordinates will be the same\n# in ACPC space which is what matters\nmontage = raw.get_montage() # the original montage in 'head' coordinates\nmontage.apply_trans(trans)\nmontage2 = raw2.get_montage() # the recovered montage in 'head' coordinates\nmontage2.apply_trans(trans2)\n\n# compare with standard\nprint(\n \"Recovered coordinate: {recovered}\\n\"\n \"Saved coordinate: {saved}\".format(\n recovered=montage2.get_positions()[\"ch_pos\"][\"LENT 1\"],\n saved=montage.get_positions()[\"ch_pos\"][\"LENT 1\"],\n )\n)" + "montage2 = raw2.get_montage()\n\n# we need to go from scanner RAS back to surface RAS (requires recon-all)\nconvert_montage_to_mri(montage2, \"sample_seeg\", subjects_dir=subjects_dir)\n\n# this uses Freesurfer recon-all subject directory\nmontage2.add_estimated_fiducials(\"sample_seeg\", subjects_dir=subjects_dir)\n\n# get head->mri trans, invert from mri->head\ntrans2 = mne.transforms.invert_transform(mne.channels.compute_native_head_t(montage2))\n\n# now the montage is properly in \"head\" and ready for analysis in MNE\nraw2.set_montage(montage2)\n\n# get the monage, apply the trans and make sure it's the same\n# note: the head coordinates may differ because they are defined by\n# the fiducials which are estimated; as long as the head->mri trans\n# is computed with the same fiducials, the coordinates will be the same\n# in ACPC space which is what matters\nmontage = raw.get_montage() # the original montage in 'head' coordinates\nmontage.apply_trans(trans)\nmontage2 = raw2.get_montage() # the recovered montage in 'head' coordinates\nmontage2.apply_trans(trans2)\n\n# compare with standard\nprint(\n f\"Recovered coordinate: {montage2.get_positions()['ch_pos']['LENT 1']}\\n\"\n f\"Saved coordinate: {montage.get_positions()['ch_pos']['LENT 1']}\"\n)" ] }, { @@ -231,7 +231,7 @@ }, "outputs": [], "source": [ - "readme = op.join(bids_root, \"README\")\nwith open(readme, \"r\", encoding=\"utf-8-sig\") as fid:\n text = fid.read()\nprint(text)" + "readme = op.join(bids_root, \"README\")\nwith open(readme, encoding=\"utf-8-sig\") as fid:\n text = fid.read()\nprint(text)" ] }, { @@ -303,7 +303,7 @@ }, "outputs": [], "source": [ - "# check that we can recover the coordinates\nprint(\n \"Recovered coordinate head: {recovered}\\n\"\n \"Original coordinate head: {original}\".format(\n recovered=raw2.info[\"chs\"][0][\"loc\"][:3], original=raw.info[\"chs\"][0][\"loc\"][:3]\n )\n)\n\n# check difference in trans\nprint(\n \"Recovered trans:\\n{recovered}\\n\"\n \"Original trans:\\n{original}\".format(\n recovered=trans2[\"trans\"].round(3),\n # combine head->mri with mri->mni to get head->mni\n # and then invert to get mni->head\n original=np.linalg.inv(np.dot(trans[\"trans\"], mri_mni_t[\"trans\"])).round(3),\n )\n)\n\n# ensure that the data in MNI coordinates is exactly the same\n# (within computer precision)\nmontage2 = raw2.get_montage() # get montage after transformed back to head\nmontage2.apply_trans(trans2)\nprint(\n \"Recovered coordinate: {recovered}\\n\"\n \"Original coordinate: {original}\".format(\n recovered=montage2.get_positions()[\"ch_pos\"][\"LENT 1\"],\n original=montage.get_positions()[\"ch_pos\"][\"LENT 1\"],\n )\n)" + "# check that we can recover the coordinates\nprint(\n \"Recovered coordinate head: {recovered}\\n\"\n \"Original coordinate head: {original}\".format(\n recovered=raw2.info[\"chs\"][0][\"loc\"][:3], original=raw.info[\"chs\"][0][\"loc\"][:3]\n )\n)\n\n# check difference in trans\nprint(\n f\"Recovered trans:\\n{trans2['trans'].round(3)}\\n\"\n # combine head->mri with mri->mni to get head->mni\n # and then invert to get mni->head\n \"Original trans:\\n\"\n f\"{np.linalg.inv(np.dot(trans['trans'], mri_mni_t['trans'])).round(3)}\"\n)\n\n# ensure that the data in MNI coordinates is exactly the same\n# (within computer precision)\nmontage2 = raw2.get_montage() # get montage after transformed back to head\nmontage2.apply_trans(trans2)\nprint(\n f\"Recovered coordinate: {montage2.get_positions()['ch_pos']['LENT 1']}\\n\"\n f\"Original coordinate: {montage.get_positions()['ch_pos']['LENT 1']}\"\n)" ] }, { @@ -364,7 +364,7 @@ }, "outputs": [], "source": [ - "montage2 = raw2.get_montage() # get montage after transformed back to head\nmontage2.apply_trans(trans2) # apply trans to go back to 'mri'\nprint(\n \"Recovered coordinate: {recovered}\\n\"\n \"Original coordinate: {original}\".format(\n recovered=montage2.get_positions()[\"ch_pos\"][\"LENT 1\"],\n original=montage.get_positions()[\"ch_pos\"][\"LENT 1\"],\n )\n)" + "montage2 = raw2.get_montage() # get montage after transformed back to head\nmontage2.apply_trans(trans2) # apply trans to go back to 'mri'\nprint(\n f\"Recovered coordinate: {montage2.get_positions()['ch_pos']['LENT 1']}\\n\"\n f\"Original coordinate: {montage.get_positions()['ch_pos']['LENT 1']}\"\n)" ] }, { diff --git a/dev/_downloads/d5b79ff106a037057e89cb5616b1b839/anonymize_dataset.py b/dev/_downloads/d5b79ff106a037057e89cb5616b1b839/anonymize_dataset.py index 3760d4078..af821c774 100644 --- a/dev/_downloads/d5b79ff106a037057e89cb5616b1b839/anonymize_dataset.py +++ b/dev/_downloads/d5b79ff106a037057e89cb5616b1b839/anonymize_dataset.py @@ -24,15 +24,17 @@ # %% import shutil from pathlib import Path + import mne + from mne_bids import ( BIDSPath, - write_raw_bids, + anonymize_dataset, + print_dir_tree, write_anat, write_meg_calibration, write_meg_crosstalk, - anonymize_dataset, - print_dir_tree, + write_raw_bids, ) data_path = Path(mne.datasets.sample.data_path()) diff --git a/dev/_downloads/f336dfe6a8ab84474813b87342e0c0a3/convert_empty_room.py b/dev/_downloads/f336dfe6a8ab84474813b87342e0c0a3/convert_empty_room.py index 5cca3d9d8..0b56e9288 100644 --- a/dev/_downloads/f336dfe6a8ab84474813b87342e0c0a3/convert_empty_room.py +++ b/dev/_downloads/f336dfe6a8ab84474813b87342e0c0a3/convert_empty_room.py @@ -31,13 +31,12 @@ import os.path as op import shutil - from datetime import datetime, timezone import mne from mne.datasets import sample -from mne_bids import write_raw_bids, read_raw_bids, BIDSPath, print_dir_tree +from mne_bids import BIDSPath, print_dir_tree, read_raw_bids, write_raw_bids # %% # And define the paths and event_id dictionary. diff --git a/dev/_modules/mne_bids/copyfiles.html b/dev/_modules/mne_bids/copyfiles.html index 50ef35cdd..0a8ecb9f6 100644 --- a/dev/_modules/mne_bids/copyfiles.html +++ b/dev/_modules/mne_bids/copyfiles.html @@ -544,17 +544,17 @@

Source code for mne_bids.copyfiles

 # License: BSD-3-Clause
 import os
 import os.path as op
-from pathlib import Path
 import re
 import shutil as sh
+from pathlib import Path
 
-from mne.io import read_raw_brainvision, read_raw_edf, read_raw_bdf, anonymize_info
-from mne.utils import logger, verbose
 import numpy as np
+from mne.io import anonymize_info, read_raw_bdf, read_raw_brainvision, read_raw_edf
+from mne.utils import logger, verbose
 from scipy.io import loadmat, savemat
 
-from mne_bids.path import BIDSPath, _parse_ext, _mkdir_p
-from mne_bids.utils import _get_mrk_meas_date, _check_anonymize, warn
+from mne_bids.path import BIDSPath, _mkdir_p, _parse_ext
+from mne_bids.utils import _check_anonymize, _get_mrk_meas_date, warn
 
 
 def _copytree(src, dst, **kwargs):
@@ -622,7 +622,7 @@ 
Source code for mne_bids.copyfiles
     enc = _get_brainvision_encoding(vhdr_path)
 
     # ..and read it
-    with open(vhdr_path, "r", encoding=enc) as f:
+    with open(vhdr_path, encoding=enc) as f:
         lines = f.readlines()
 
     # Try to find data file .eeg/.dat
@@ -786,7 +786,7 @@ 
Source code for mne_bids.copyfiles
 def _replace_file(fname, pattern, replace):
     """Overwrite file, replacing end of lines matching pattern with replace."""
     new_content = []
-    for line in open(fname, "r"):
+    for line in open(fname):
         match = re.match(pattern, line)
         if match:
             line = match.group()[: -len(replace)] + replace + "\n"
@@ -899,14 +899,14 @@ 
Source code for mne_bids.copyfiles
         "MarkerFile=" + basename_src + ".vmrk",
     ]
 
-    with open(vhdr_src, "r", encoding=enc) as fin:
+    with open(vhdr_src, encoding=enc) as fin:
         with open(vhdr_dest, "w", encoding=enc) as fout:
             for line in fin.readlines():
                 if line.strip() in search_lines:
                     line = line.replace(basename_src, basename_dest)
                 fout.write(line)
 
-    with open(vmrk_file_path, "r", encoding=enc) as fin:
+    with open(vmrk_file_path, encoding=enc) as fin:
         with open(fname_dest + ".vmrk", "w", encoding=enc) as fout:
             for line in fin.readlines():
                 if line.strip() in search_lines:
@@ -1016,7 +1016,7 @@ 
Source code for mne_bids.copyfiles
         elif ext_src in [".edf", ".EDF"]:
             raw = read_raw_edf(dest, preload=False, verbose=0)
         else:
-            raise ValueError("Unsupported file type ({0})".format(ext_src))
+            raise ValueError(f"Unsupported file type ({ext_src})")
 
         # Get subject info, recording info, and recording date
         with open(dest, "rb") as f:
diff --git a/dev/_modules/mne_bids/dig.html b/dev/_modules/mne_bids/dig.html
index 1d8cd3095..acf260e6a 100644
--- a/dev/_modules/mne_bids/dig.html
+++ b/dev/_modules/mne_bids/dig.html
@@ -532,39 +532,39 @@ 
Source code for mne_bids.dig
 #          Alex Rockhill <aprockhill@mailbox.org>
 #
 # License: BSD-3-Clause
-import os.path as op
 import json
-from collections import OrderedDict
-from pathlib import Path
+import os.path as op
 import re
 import warnings
+from collections import OrderedDict
+from pathlib import Path
 
 import mne
 import numpy as np
 from mne.io.constants import FIFF
-from mne.utils import logger, _validate_type, _check_option, get_subjects_dir
 from mne.io.pick import _picks_to_idx
+from mne.utils import _check_option, _validate_type, get_subjects_dir, logger
 
 from mne_bids.config import (
     ALLOWED_SPACES,
+    BIDS_COORD_FRAME_DESCRIPTIONS,
     BIDS_COORDINATE_UNITS,
-    MNE_TO_BIDS_FRAMES,
+    BIDS_STANDARD_TEMPLATE_COORDINATE_SYSTEMS,
     BIDS_TO_MNE_FRAMES,
     MNE_FRAME_TO_STR,
     MNE_STR_TO_FRAME,
-    BIDS_COORD_FRAME_DESCRIPTIONS,
-    BIDS_STANDARD_TEMPLATE_COORDINATE_SYSTEMS,
+    MNE_TO_BIDS_FRAMES,
 )
+from mne_bids.path import BIDSPath
 from mne_bids.tsv_handler import _from_tsv
 from mne_bids.utils import (
+    _import_nibabel,
     _scale_coord_to_meters,
     _write_json,
     _write_tsv,
     verbose,
     warn,
-    _import_nibabel,
 )
-from mne_bids.path import BIDSPath
 
 data_dir = Path(__file__).parent / "data"
 
@@ -574,7 +574,7 @@ 
Source code for mne_bids.dig
 
     Handle xyz coordinates and coordinate frame of each channel.
     """
-    logger.info("Reading electrode " "coords from {}.".format(electrodes_fname))
+    logger.info("Reading electrode " f"coords from {electrodes_fname}.")
     electrodes_dict = _from_tsv(electrodes_fname)
     ch_names_tsv = electrodes_dict["name"]
 
@@ -608,7 +608,7 @@ 
Source code for mne_bids.dig
     Handle reading the coordinate frame and coordinate unit
     of each electrode.
     """
-    with open(coordsystem_fpath, "r", encoding="utf-8-sig") as fin:
+    with open(coordsystem_fpath, encoding="utf-8-sig") as fin:
         coordsystem_json = json.load(fin)
 
     if datatype == "meg":
@@ -706,7 +706,7 @@ 
Source code for mne_bids.dig
             ]
         )
     else:  # pragma: no cover
-        raise RuntimeError("datatype {} not supported.".format(datatype))
+        raise RuntimeError(f"datatype {datatype} not supported.")
 
     # Add impedance values if available, currently only BrainVision:
     # https://github.com/mne-tools/mne-python/pull/7974
@@ -903,7 +903,7 @@ 
Source code for mne_bids.dig
     # XXX: improve later when BIDS is updated
     # check that there already exists a coordsystem.json
     if Path(fname).exists() and not overwrite:
-        with open(fname, "r", encoding="utf-8-sig") as fin:
+        with open(fname, encoding="utf-8-sig") as fin:
             coordsystem_dict = json.load(fin)
         if fid_json != coordsystem_dict:
             raise RuntimeError(
diff --git a/dev/_modules/mne_bids/inspect.html b/dev/_modules/mne_bids/inspect.html
index d07968304..fa4cd64d6 100644
--- a/dev/_modules/mne_bids/inspect.html
+++ b/dev/_modules/mne_bids/inspect.html
@@ -534,18 +534,16 @@ 
Source code for mne_bids.inspect
 
 from pathlib import Path
 
-import numpy as np
-
 import mne
-
+import numpy as np
+from mne.preprocessing import annotate_amplitude
 from mne.utils import logger, verbose
 from mne.viz import use_browser_backend
-from mne.preprocessing import annotate_amplitude
 
-from mne_bids import read_raw_bids, mark_channels
+from mne_bids import mark_channels, read_raw_bids
+from mne_bids.config import ALLOWED_DATATYPE_EXTENSIONS
 from mne_bids.read import _from_tsv, _read_events
 from mne_bids.write import _events_tsv
-from mne_bids.config import ALLOWED_DATATYPE_EXTENSIONS
 
 
 

diff --git a/dev/_modules/mne_bids/path.html b/dev/_modules/mne_bids/path.html
index 823221342..78dfa8d33 100644
--- a/dev/_modules/mne_bids/path.html
+++ b/dev/_modules/mne_bids/path.html
@@ -532,40 +532,40 @@ 
Source code for mne_bids.path
 #
 # License: BSD-3-Clause
 import glob
+import json
 import os
 import re
-from io import StringIO
 import shutil as sh
 from copy import deepcopy
+from datetime import datetime
+from io import StringIO
 from os import path as op
 from pathlib import Path
-from datetime import datetime
-import json
 from textwrap import indent
 from typing import Optional
 
 import numpy as np
-from mne.utils import logger, _validate_type, verbose, _check_fname
+from mne.utils import _check_fname, _validate_type, logger, verbose
 
 from mne_bids.config import (
-    ALLOWED_PATH_ENTITIES,
+    ALLOWED_DATATYPE_EXTENSIONS,
+    ALLOWED_DATATYPES,
     ALLOWED_FILENAME_EXTENSIONS,
     ALLOWED_FILENAME_SUFFIX,
+    ALLOWED_PATH_ENTITIES,
     ALLOWED_PATH_ENTITIES_SHORT,
-    ALLOWED_DATATYPES,
-    ALLOWED_DATATYPE_EXTENSIONS,
     ALLOWED_SPACES,
-    reader,
     ENTITY_VALUE_TYPE,
+    reader,
 )
+from mne_bids.tsv_handler import _drop, _from_tsv, _to_tsv
 from mne_bids.utils import (
-    _check_key_val,
     _check_empty_room_basename,
-    param_regex,
+    _check_key_val,
     _ensure_tuple,
+    param_regex,
     warn,
 )
-from mne_bids.tsv_handler import _from_tsv, _drop, _to_tsv
 
 
 def _find_empty_room_candidates(bids_path):
@@ -704,7 +704,7 @@ 
Source code for mne_bids.path
 
 

 [docs]
-class BIDSPath(object):
+class BIDSPath:
     """A BIDS path object.
 
     BIDS filename prefixes have one or more pieces of metadata in them. They
@@ -1507,7 +1507,7 @@ 
Source code for mne_bids.path
                 if isinstance(val, str) and not val.isdigit():
                     raise ValueError(f"{key} is not an index (Got {val})")
                 elif isinstance(val, int):
-                    kwargs[key] = "{:02}".format(val)
+                    kwargs[key] = f"{val:02}"
 
         # ensure extension starts with a '.'
         extension = kwargs.get("extension")
@@ -1714,7 +1714,7 @@ 
Source code for mne_bids.path
             .update(datatype=None, suffix="meg")
             .find_matching_sidecar(extension=".json")
         )
-        with open(sidecar_fname, "r", encoding="utf-8") as f:
+        with open(sidecar_fname, encoding="utf-8") as f:
             sidecar_json = json.load(f)
 
         if "AssociatedEmptyRoom" in sidecar_json:
@@ -1945,7 +1945,7 @@ 
Source code for mne_bids.path
         prints to the console, else a string is printed to.
     """
     entry_lines = list()
-    with open(file, "r", encoding="utf-8-sig") as fid:
+    with open(file, encoding="utf-8-sig") as fid:
         if is_tsv:  # format tsv files nicely
             header = _truncate_tsv_line(fid.readline())
             if line_numbers:
@@ -2096,7 +2096,7 @@ 
Source code for mne_bids.path
         # Only print if this is up to the depth we asked
         if branchlen <= max_depth:
             if branchlen <= 1:
-                print("|{}".format(op.basename(root) + os.sep), file=outfile)
+                print(f"|{op.basename(root) + os.sep}", file=outfile)
             else:
                 print(
                     "|{} {}".format(
@@ -2627,7 +2627,7 @@ 
Source code for mne_bids.path
     ]
     ignore_dirs = _ensure_tuple(existing_ignore_dirs)
 
-    p = re.compile(r"{}-(.*?)_".format(entity_long_abbr_map[entity_key]))
+    p = re.compile(rf"{entity_long_abbr_map[entity_key]}-(.*?)_")
     values = list()
     filenames = root.glob(f"**/*{entity_long_abbr_map[entity_key]}-*_*")
 
diff --git a/dev/_modules/mne_bids/read.html b/dev/_modules/mne_bids/read.html
index b5ab06856..daf884dff 100644
--- a/dev/_modules/mne_bids/read.html
+++ b/dev/_modules/mne_bids/read.html
@@ -534,38 +534,37 @@ 
Source code for mne_bids.read
 #          Stefan Appelhoff <stefan.appelhoff@mailbox.org>
 #
 # License: BSD-3-Clause
-import os.path as op
-from pathlib import Path
 import json
+import os
+import os.path as op
 import re
 from datetime import datetime, timezone
 from difflib import get_close_matches
-import os
+from pathlib import Path
 
-import numpy as np
 import mne
-from mne import io, read_events, events_from_annotations
-from mne import pick_channels_regexp
-from mne.utils import logger, get_subjects_dir
+import numpy as np
+from mne import events_from_annotations, io, pick_channels_regexp, read_events
 from mne.coreg import fit_matched_points
 from mne.transforms import apply_trans
+from mne.utils import get_subjects_dir, logger
 
-from mne_bids.dig import _read_dig_bids
-from mne_bids.tsv_handler import _from_tsv, _drop
 from mne_bids.config import (
     ALLOWED_DATATYPE_EXTENSIONS,
     ANNOTATIONS_TO_KEEP,
-    reader,
     _map_options,
+    reader,
 )
-from mne_bids.utils import _get_ch_type_mapping, verbose, warn, _import_nibabel
+from mne_bids.dig import _read_dig_bids
 from mne_bids.path import (
     BIDSPath,
-    _parse_ext,
     _find_matching_sidecar,
     _infer_datatype,
+    _parse_ext,
     get_bids_path_from_fname,
 )
+from mne_bids.tsv_handler import _drop, _from_tsv
+from mne_bids.utils import _get_ch_type_mapping, _import_nibabel, verbose, warn
 
 
 def _read_raw(
@@ -885,7 +884,7 @@ 
Source code for mne_bids.read
 
     Handle PowerLineFrequency of recording.
     """
-    with open(sidecar_fname, "r", encoding="utf-8-sig") as fin:
+    with open(sidecar_fname, encoding="utf-8-sig") as fin:
         sidecar_json = json.load(fin)
 
     # read in the sidecar JSON's and raw object's line frequency
@@ -984,7 +983,7 @@ 
Source code for mne_bids.read
 
     Handle onset, duration, and description of each event.
     """
-    logger.info("Reading events from {}.".format(events_fname))
+    logger.info(f"Reading events from {events_fname}.")
     events_dict = _from_tsv(events_fname)
 
     # Get the descriptions of the events
@@ -1094,7 +1093,7 @@ 
Source code for mne_bids.read
 
     Updates status (bad) and types of channels.
     """
-    logger.info("Reading channel info from {}.".format(channels_fname))
+    logger.info(f"Reading channel info from {channels_fname}.")
     channels_dict = _from_tsv(channels_fname)
     ch_names_tsv = channels_dict["name"]
 
diff --git a/dev/_modules/mne_bids/report/_report.html b/dev/_modules/mne_bids/report/_report.html
index b964a4bb1..b7d020c3b 100644
--- a/dev/_modules/mne_bids/report/_report.html
+++ b/dev/_modules/mne_bids/report/_report.html
@@ -535,23 +535,22 @@ 
Source code for mne_bids.report._report
 import textwrap
 from pathlib import Path
 
-import numpy as np
 import jinja2
+import numpy as np
 from mne.utils import logger, verbose
 
-from mne_bids.config import DOI, ALLOWED_DATATYPES
-from mne_bids.tsv_handler import _from_tsv
+from mne_bids.config import ALLOWED_DATATYPES, DOI
 from mne_bids.path import (
+    BIDSPath,
+    _find_matching_sidecar,
+    _parse_ext,
     get_bids_path_from_fname,
     get_datatypes,
     get_entity_vals,
-    BIDSPath,
-    _parse_ext,
-    _find_matching_sidecar,
 )
+from mne_bids.tsv_handler import _from_tsv
 from mne_bids.utils import warn
 
-
 jinja_env = jinja2.Environment(
     loader=jinja2.PackageLoader(
         package_name="mne_bids.report", package_path="templates"
@@ -684,7 +683,7 @@ 
Source code for mne_bids.report._report
         return dict()
 
     # read file and 'REQUIRED' components of it
-    with open(dataset_descrip_fpath, "r", encoding="utf-8-sig") as fin:
+    with open(dataset_descrip_fpath, encoding="utf-8-sig") as fin:
         dataset_description = json.load(fin)
 
     # create dictionary to pass into template string
@@ -858,7 +857,7 @@ 
Source code for mne_bids.report._report
             sidecar_fname = _find_matching_sidecar(
                 bids_path=bids_path, suffix=datatype, extension=".json"
             )
-            with open(sidecar_fname, "r", encoding="utf-8-sig") as fin:
+            with open(sidecar_fname, encoding="utf-8-sig") as fin:
                 sidecar_json = json.load(fin)
 
             # aggregate metadata from each scan
diff --git a/dev/_modules/mne_bids/sidecar_updates.html b/dev/_modules/mne_bids/sidecar_updates.html
index 21d405633..e51e1c572 100644
--- a/dev/_modules/mne_bids/sidecar_updates.html
+++ b/dev/_modules/mne_bids/sidecar_updates.html
@@ -538,11 +538,10 @@ 
Source code for mne_bids.sidecar_updates
 from collections import OrderedDict
 
 import numpy as np
-
 from mne.channels import DigMontage, make_dig_montage
-from mne.utils import logger, _validate_type, verbose, _check_on_missing, _on_missing
 from mne.io import read_fiducials
 from mne.io.constants import FIFF
+from mne.utils import _check_on_missing, _on_missing, _validate_type, logger, verbose
 
 from mne_bids import BIDSPath
 from mne_bids.utils import _write_json
@@ -637,14 +636,14 @@ 
Source code for mne_bids.sidecar_updates
     if isinstance(entries, dict):
         sidecar_tmp = entries
     else:
-        with open(entries, "r") as tmp_f:
+        with open(entries) as tmp_f:
             sidecar_tmp = json.load(tmp_f, object_pairs_hook=OrderedDict)
 
     logger.debug(sidecar_tmp)
     logger.debug(f"Updating {fpath}...")
 
     # load in sidecar filepath
-    with open(fpath, "r") as tmp_f:
+    with open(fpath) as tmp_f:
         sidecar_json = json.load(tmp_f, object_pairs_hook=OrderedDict)
 
     # update sidecar JSON file with the fields passed in
@@ -667,7 +666,7 @@ 
Source code for mne_bids.sidecar_updates
     val : str
         The corresponding value to change to in the sidecar JSON file.
     """
-    with open(sidecar_fname, "r", encoding="utf-8-sig") as fin:
+    with open(sidecar_fname, encoding="utf-8-sig") as fin:
         sidecar_json = json.load(fin)
     sidecar_json[key] = val
     _write_json(sidecar_fname, sidecar_json, overwrite=True)
@@ -881,9 +880,9 @@ 
Source code for mne_bids.sidecar_updates
     """Get anatomical landmarks from fiducials file, in MRI voxel space."""
     # avoid dicrular imports
     from mne_bids.write import (
+        _get_fid_coords,
         _get_t1w_mgh,
         _mri_landmarks_to_mri_voxels,
-        _get_fid_coords,
     )
 
     digpoints, coord_frame = read_fiducials(fname)
@@ -911,7 +910,8 @@ 
Source code for mne_bids.sidecar_updates
 
     t1w_mgh = _get_t1w_mgh(fs_subject, fs_subjects_dir)
     landmark_coords_voxels = _mri_landmarks_to_mri_voxels(
-        mri_landmarks=landmark_coords_mri * 1000, t1_mgh=t1w_mgh  # in mm
+        mri_landmarks=landmark_coords_mri * 1000,
+        t1_mgh=t1w_mgh,  # in mm
     )
     montage_voxels = make_dig_montage(
         lpa=landmark_coords_voxels[0],
diff --git a/dev/_modules/mne_bids/utils.html b/dev/_modules/mne_bids/utils.html
index c58ba8e35..a2e0c231a 100644
--- a/dev/_modules/mne_bids/utils.html
+++ b/dev/_modules/mne_bids/utils.html
@@ -538,18 +538,18 @@ 
Source code for mne_bids.utils
 import json
 import os
 import re
-from datetime import datetime, date, timedelta, timezone
+from datetime import date, datetime, timedelta, timezone
 from os import path as op
 
 import numpy as np
+from mne import pick_types
 from mne.channels import make_standard_montage
 from mne.io.kit.kit import get_kit_info
-from mne import pick_types
-from mne.utils import warn as _warn, logger, verbose
+from mne.utils import logger, verbose
+from mne.utils import warn as _warn
 
 from mne_bids.tsv_handler import _to_tsv
 
-
 # This regex matches key-val pairs. Any characters are allowed in the key and
 # the value, except these special symbols: - _ . \ /
 param_regex = re.compile(r"([^-_\.\\\/]+)-([^-_\.\\\/]+)")
@@ -645,7 +645,7 @@ 
Source code for mne_bids.utils
         raise ValueError(
             "Only two types of mappings are currently supported: "
             "from mne to bids, or from bids to mne. However, "
-            'you specified from "{}" to "{}"'.format(fro, to)
+            f'you specified from "{fro}" to "{to}"'
         )
 
     return mapping
diff --git a/dev/_modules/mne_bids/write.html b/dev/_modules/mne_bids/write.html
index b733b5095..770fc0fb9 100644
--- a/dev/_modules/mne_bids/write.html
+++ b/dev/_modules/mne_bids/write.html
@@ -535,92 +535,89 @@ 
Source code for mne_bids.write
 #          Matt Sanderson <matt.sanderson@mq.edu.au>
 #
 # License: BSD-3-Clause
-from typing import List
 import json
-import re
-import sys
 import os
 import os.path as op
-from pathlib import Path
-from datetime import datetime, timezone, timedelta
+import re
 import shutil
-from collections import defaultdict, OrderedDict
+import sys
 import warnings
+from collections import OrderedDict, defaultdict
+from datetime import datetime, timedelta, timezone
+from pathlib import Path
 
-import numpy as np
-from scipy import linalg
 import mne
-from mne.transforms import _get_trans, apply_trans, rotation, translation
+import mne.preprocessing
+import numpy as np
 from mne import Epochs, channel_type
+from mne.channels.channels import _get_meg_system, _unit2human
+from mne.chpi import get_chpi_info
+from mne.io import BaseRaw, read_fiducials
 from mne.io.constants import FIFF
 from mne.io.pick import _picks_to_idx
-from mne.io import BaseRaw, read_fiducials
-from mne.channels.channels import _unit2human, _get_meg_system
-from mne.chpi import get_chpi_info
+from mne.transforms import _get_trans, apply_trans, rotation, translation
 from mne.utils import (
-    check_version,
-    logger,
     Bunch,
+    ProgressBar,
     _validate_type,
+    check_version,
     get_subjects_dir,
+    logger,
     verbose,
-    ProgressBar,
 )
-import mne.preprocessing
+from scipy import linalg
 
-from mne_bids.pick import coil_type
-from mne_bids.dig import _write_dig_bids, _write_coordsystem_json
-from mne_bids.utils import (
-    _write_json,
-    _write_tsv,
-    _write_text,
-    _age_on_date,
-    _infer_eeg_placement_scheme,
-    _get_ch_type_mapping,
-    _check_anonymize,
-    _stamp_to_dt,
-    _handle_datatype,
-    warn,
-    _import_nibabel,
-)
 from mne_bids import (
     BIDSPath,
-    read_raw_bids,
     get_anonymization_daysback,
     get_bids_path_from_fname,
+    read_raw_bids,
+)
+from mne_bids.config import (
+    ALLOWED_DATATYPE_EXTENSIONS,
+    ALLOWED_INPUT_EXTENSIONS,
+    ANONYMIZED_JSON_KEY_WHITELIST,
+    BIDS_STANDARD_TEMPLATE_COORDINATE_SYSTEMS,
+    BIDS_VERSION,
+    CONVERT_FORMATS,
+    EXT_TO_UNIT_MAP,
+    IGNORED_CHANNELS,
+    MANUFACTURERS,
+    ORIENTATION,
+    PYBV_VERSION,
+    REFERENCES,
+    UNITS_MNE_TO_BIDS_MAP,
+    _map_options,
+    reader,
 )
-from mne_bids.path import _parse_ext, _mkdir_p, _path_to_str
 from mne_bids.copyfiles import (
     copyfile_brainvision,
-    copyfile_eeglab,
-    copyfile_ctf,
     copyfile_bti,
-    copyfile_kit,
+    copyfile_ctf,
     copyfile_edf,
+    copyfile_eeglab,
+    copyfile_kit,
 )
-from mne_bids.tsv_handler import _from_tsv, _drop, _contains_row, _combine_rows
+from mne_bids.dig import _write_coordsystem_json, _write_dig_bids
+from mne_bids.path import _mkdir_p, _parse_ext, _path_to_str
+from mne_bids.pick import coil_type
 from mne_bids.read import _find_matching_sidecar, _read_events
 from mne_bids.sidecar_updates import update_sidecar_json
-
-from mne_bids.config import (
-    ORIENTATION,
-    EXT_TO_UNIT_MAP,
-    MANUFACTURERS,
-    IGNORED_CHANNELS,
-    ALLOWED_DATATYPE_EXTENSIONS,
-    BIDS_VERSION,
-    REFERENCES,
-    _map_options,
-    reader,
-    ALLOWED_INPUT_EXTENSIONS,
-    CONVERT_FORMATS,
-    ANONYMIZED_JSON_KEY_WHITELIST,
-    PYBV_VERSION,
-    BIDS_STANDARD_TEMPLATE_COORDINATE_SYSTEMS,
-    UNITS_MNE_TO_BIDS_MAP,
+from mne_bids.tsv_handler import _combine_rows, _contains_row, _drop, _from_tsv
+from mne_bids.utils import (
+    _age_on_date,
+    _check_anonymize,
+    _get_ch_type_mapping,
+    _handle_datatype,
+    _import_nibabel,
+    _infer_eeg_placement_scheme,
+    _stamp_to_dt,
+    _write_json,
+    _write_text,
+    _write_tsv,
+    warn,
 )
 
-
 _FIFF_SPLIT_SIZE = "2GB"  # MNE-Python default; can be altered during debugging
 
 
@@ -910,7 +907,7 @@ 
Source code for mne_bids.write
         already contains that citation.
     """
     if os.path.isfile(fname) and not overwrite:
-        with open(fname, "r", encoding="utf-8-sig") as fid:
+        with open(fname, encoding="utf-8-sig") as fid:
             orig_data = fid.read()
         mne_bids_ref = REFERENCES["mne-bids"] in orig_data
         datatype_ref = REFERENCES[datatype] in orig_data
@@ -1204,9 +1201,9 @@ 
Source code for mne_bids.write
             # so load the file from the specified location. We do this
             # here to keep the try block as short as possible.
             raise ValueError(
-                "`{}` must be a path to an MRI data "
+                f"`{name}` must be a path to an MRI data "
                 "file or a nibabel image object, but it "
-                'is of type "{}"'.format(name, type(image))
+                f'is of type "{type(image)}"'
             )
         else:
             image = nib.load(image)
@@ -1859,7 +1856,7 @@ 
Source code for mne_bids.write
 
     # Handle potentially existing file contents
     if op.isfile(fname):
-        with open(fname, "r", encoding="utf-8-sig") as fin:
+        with open(fname, encoding="utf-8-sig") as fin:
             orig_cols = json.load(fin)
         if "BIDSVersion" in orig_cols and orig_cols["BIDSVersion"] != BIDS_VERSION:
             warnings.warn(
@@ -2962,9 +2959,9 @@ 
Source code for mne_bids.write
         img_json = {"AnatomicalLandmarkCoordinates": img_json}
         fname = bids_path.copy().update(extension=".json")
         if op.isfile(fname) and not overwrite:
-            raise IOError(
+            raise OSError(
                 "Wanted to write a file but it already exists and "
-                '`overwrite` is set to False. File: "{}"'.format(fname)
+                f'`overwrite` is set to False. File: "{fname}"'
             )
         _write_json(fname, img_json, overwrite)
 
@@ -2981,7 +2978,7 @@ 
Source code for mne_bids.write
         if overwrite:
             os.remove(bids_path)
         else:
-            raise IOError(
+            raise OSError(
                 f"Wanted to write a file but it already exists and "
                 f'`overwrite` is set to False. File: "{bids_path}"'
             )
@@ -3254,7 +3251,7 @@ 
Source code for mne_bids.write
 
 
 def _get_daysback(
-    *, bids_paths: List[BIDSPath], rng: np.random.Generator, show_progress_thresh: int
+    *, bids_paths: list[BIDSPath], rng: np.random.Generator, show_progress_thresh: int
 ) -> int:
     """Try to find a suitable "daysback" for anonymization.
 
diff --git a/dev/auto_examples/anonymize_dataset.html b/dev/auto_examples/anonymize_dataset.html
index a7e6681b9..3759cfb57 100644
--- a/dev/auto_examples/anonymize_dataset.html
+++ b/dev/auto_examples/anonymize_dataset.html
@@ -583,15 +583,17 @@
 

 
import shutil
 from pathlib import Path
+
 import mne
+
 from mne_bids import (
     BIDSPath,
-    write_raw_bids,
+    anonymize_dataset,
+    print_dir_tree,
     write_anat,
     write_meg_calibration,
     write_meg_crosstalk,
-    anonymize_dataset,
-    print_dir_tree,
+    write_raw_bids,
 )
 
 data_path = Path(mne.datasets.sample.data_path())
@@ -686,7 +688,7 @@ 
Basic anonymizationSpecifying subject IDsSpecifying subject IDsSpecifying subject IDs

 

 
@@ -941,9 +943,9 @@ 
ReproducibilityTotal running time of the script: (0 minutes 15.995 seconds)

+
Total running time of the script: (0 minutes 11.044 seconds)

 

 

@@ -611,8 +611,6 @@ 
Download the data
Using default location ~/mne_data for EEGBCI...
-Downloading EEGBCI data
-Download complete in 01s (1.2 MB)
 
 [PosixPath('/home/circleci/mne_data/MNE-eegbci-data/files/eegmmidb/1.0.0/S001/S001R02.edf')]
 

@@ -632,6 +630,13 @@ 
Download the dataEuropean Data Format with
@@ -694,1046 +699,6 @@ 
Convert to BIDS
Using default location ~/mne_data for testing...
-Dataset testing version 0.0 out of date, latest version is 0.150
-
-0.00B [00:00, ?B/s]
-632kB [00:00, 6.27MB/s]
-1.26MB [00:00, 6.15MB/s]
-1.89MB [00:00, 6.08MB/s]
-2.50MB [00:00, 6.04MB/s]
-3.13MB [00:00, 6.04MB/s]
-3.73MB [00:00, 6.00MB/s]
-4.34MB [00:00, 5.99MB/s]
-4.95MB [00:00, 5.97MB/s]
-5.57MB [00:00, 5.98MB/s]
-6.17MB [00:01, 5.88MB/s]
-6.77MB [00:01, 5.68MB/s]
-7.39MB [00:01, 5.83MB/s]
-7.98MB [00:01, 5.83MB/s]
-8.59MB [00:01, 5.91MB/s]
-9.19MB [00:01, 5.86MB/s]
-9.84MB [00:01, 5.96MB/s]
-10.5MB [00:01, 6.05MB/s]
-11.1MB [00:01, 5.98MB/s]
-11.8MB [00:01, 6.26MB/s]
-12.4MB [00:02, 6.29MB/s]
-13.1MB [00:02, 6.32MB/s]
-13.8MB [00:02, 6.43MB/s]
-14.8MB [00:02, 7.53MB/s]
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 <Figure size 640x640 with 1 Axes>
 

@@ -2157,16 +1122,16 @@ 
Cite mne-bids
readme = op.join(bids_root, "README")
-with open(readme, "r", encoding="utf-8-sig") as fid:
+with open(readme, encoding="utf-8-sig") as fid:
     text = fid.read()
 print(text)
 

 

 
References
 ----------
-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. and Jas, M. (2019). MNE-BIDS: Organizing electrophysiological data into the BIDS format and facilitating their analysis. Journal of Open Source Software 4: (1896). https://doi.org/10.21105/joss.01896
+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. and Jas, M. (2019). MNE-BIDS: Organizing electrophysiological data into the BIDS format and facilitating their analysis. Journal of Open Source Software 4: (1896).https://doi.org/10.21105/joss.01896
 
-Pernet, C. R., Appelhoff, S., Gorgolewski, K. J., Flandin, G., Phillips, C., Delorme, A., Oostenveld, R. (2019). EEG-BIDS, an extension to the brain imaging data structure for electroencephalography. Scientific Data, 6, 103. https://doi.org/10.1038/s41597-019-0104-8
+Pernet, C. R., Appelhoff, S., Gorgolewski, K. J., Flandin, G., Phillips, C., Delorme, A., Oostenveld, R. (2019). EEG-BIDS, an extension to the brain imaging data structure for electroencephalography. Scientific Data, 6, 103.https://doi.org/10.1038/s41597-019-0104-8
 

 

 
Now it’s time to manually check the BIDS directory and the meta files to add
@@ -2178,7 +1143,7 @@ 
Cite mne-bidshttps://bids-standard.github.io/bids-validator/

 
Command line tool: https://www.npmjs.com/package/bids-validator

-
Total running time of the script: (2 minutes 47.564 seconds)

+
Total running time of the script: (0 minutes 0.596 seconds)

 

 

-
Total running time of the script: (0 minutes 2.900 seconds)

+
Total running time of the script: (0 minutes 1.844 seconds)

 

@@ -613,12 +613,6 @@
 data_dir = op.join(mne_data_dir, "MNE-eegbci-data")
 

 

-
Downloading EEGBCI data
-Download complete in 08s (7.4 MB)
-Downloading EEGBCI data
-Download complete in 08s (7.3 MB)
-

-

 
Let us loop over the subjects and create BIDS-compatible folder

 
# Make a path where we can save the data to
 bids_root = op.join(mne_data_dir, "eegmmidb_bids_group_conversion")
@@ -973,7 +967,7 @@
 0.0 were removed from analysis).
 

 

-
Total running time of the script: (0 minutes 18.918 seconds)

+
Total running time of the script: (0 minutes 2.126 seconds)

 

 

 
import os.path as op
-import numpy as np
 import shutil
 
+import mne
 import nibabel as nib
+import numpy as np
 from nilearn.plotting import plot_anat
 
-import mne
 from mne_bids import (
     BIDSPath,
-    write_raw_bids,
-    write_anat,
+    convert_montage_to_mri,
+    convert_montage_to_ras,
     get_anat_landmarks,
+    print_dir_tree,
     read_raw_bids,
     search_folder_for_text,
-    print_dir_tree,
     template_to_head,
-    convert_montage_to_ras,
-    convert_montage_to_mri,
+    write_anat,
+    write_raw_bids,
 )
 

 

@@ -630,179 +630,6 @@ 
Step 1: Download the data
Using default location ~/mne_data for misc...
-Dataset misc version 0.0 out of date, latest version is 0.26
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-Download complete in 29s (278.8 MB)
 Opening raw data file /home/circleci/mne_data/MNE-misc-data/seeg/sample_seeg_ieeg.fif...
     Range : 1310640 ... 1370605 =   1311.411 ...  1371.411 secs
 Ready.
@@ -1333,16 +1160,13 @@ 
Step 3: Load channels from BIDS-formatted dataset and compare# compare with standard
 print(
-    "Recovered coordinate: {recovered}\n"
-    "Saved coordinate:     {saved}".format(
-        recovered=montage2.get_positions()["ch_pos"]["LENT 1"],
-        saved=montage.get_positions()["ch_pos"]["LENT 1"],
-    )
+    f"Recovered coordinate: {montage2.get_positions()['ch_pos']['LENT 1']}\n"
+    f"Saved coordinate: {montage.get_positions()['ch_pos']['LENT 1']}"
 )
 

 

 
Recovered coordinate: [-0.02430001  0.02610001 -0.05600001]
-Saved coordinate:     [-0.0243  0.0261 -0.056 ]
+Saved coordinate: [-0.0243  0.0261 -0.056 ]
 

 

 
@@ -1352,14 +1176,14 @@ 
Step 4: Cite mne-bids
 
readme = op.join(bids_root, "README")
-with open(readme, "r", encoding="utf-8-sig") as fid:
+with open(readme, encoding="utf-8-sig") as fid:
     text = fid.read()
 print(text)
 

 

 
References
 ----------
-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. and Jas, M. (2019). MNE-BIDS: Organizing electrophysiological data into the BIDS format and facilitating their analysis. Journal of Open Source Software 4: (1896). https://doi.org/10.21105/joss.01896
+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. and Jas, M. (2019). MNE-BIDS: Organizing electrophysiological data into the BIDS format and facilitating their analysis. Journal of Open Source Software 4: (1896).https://doi.org/10.21105/joss.01896
 
 Holdgraf, C., Appelhoff, S., Bickel, S., Bouchard, K., D'Ambrosio, S., David, O., … Hermes, D. (2019). iEEG-BIDS, extending the Brain Imaging Data Structure specification to human intracranial electrophysiology. Scientific Data, 6, 102. https://doi.org/10.1038/s41597-019-0105-7
 

@@ -1425,7 +1249,7 @@ 
Step 5: Store coordinates in a template space
Opening raw data file /home/circleci/mne_data/MNE-misc-data/seeg/sample_seeg_ieeg.fif...
     Range : 1310640 ... 1370605 =   1311.411 ...  1371.411 secs
 Ready.
-/home/circleci/project/examples/convert_ieeg_to_bids.py:357: RuntimeWarning: Converting data files to BrainVision format for anonymization
+/home/circleci/project/examples/convert_ieeg_to_bids.py:354: RuntimeWarning: Converting data files to BrainVision format for anonymization
   write_raw_bids(
 Writing '/home/circleci/mne_data/ieeg_bids/README'...
 Writing '/home/circleci/mne_data/ieeg_bids/participants.tsv'...
@@ -1439,7 +1263,7 @@ 
Step 5: Store coordinates in a template space# check difference in trans
 print(
-    "Recovered trans:\n{recovered}\n"
-    "Original trans:\n{original}".format(
-        recovered=trans2["trans"].round(3),
-        # combine head->mri with mri->mni to get head->mni
-        # and then invert to get mni->head
-        original=np.linalg.inv(np.dot(trans["trans"], mri_mni_t["trans"])).round(3),
-    )
+    f"Recovered trans:\n{trans2['trans'].round(3)}\n"
+    # combine head->mri with mri->mni to get head->mni
+    # and then invert to get mni->head
+    "Original trans:\n"
+    f"{np.linalg.inv(np.dot(trans['trans'], mri_mni_t['trans'])).round(3)}"
 )
 
 # ensure that the data in MNI coordinates is exactly the same
@@ -1497,11 +1319,8 @@ 
Step 5: Store coordinates in a template spacemontage2 = raw2.get_montage()  # get montage after transformed back to head
 montage2.apply_trans(trans2)
 print(
-    "Recovered coordinate: {recovered}\n"
-    "Original coordinate:  {original}".format(
-        recovered=montage2.get_positions()["ch_pos"]["LENT 1"],
-        original=montage.get_positions()["ch_pos"]["LENT 1"],
-    )
+    f"Recovered coordinate: {montage2.get_positions()['ch_pos']['LENT 1']}\n"
+    f"Original coordinate: {montage.get_positions()['ch_pos']['LENT 1']}"
 )
 

 

@@ -1518,7 +1337,7 @@ 
Step 5: Store coordinates in a template spaceraw object are slightly off.
@@ -1611,7 +1430,7 @@ 
Step 5: Store coordinates in a template space
montage2 = raw2.get_montage()  # get montage after transformed back to head
 montage2.apply_trans(trans2)  # apply trans to go back to 'mri'
 print(
-    "Recovered coordinate: {recovered}\n"
-    "Original coordinate:  {original}".format(
-        recovered=montage2.get_positions()["ch_pos"]["LENT 1"],
-        original=montage.get_positions()["ch_pos"]["LENT 1"],
-    )
+    f"Recovered coordinate: {montage2.get_positions()['ch_pos']['LENT 1']}\n"
+    f"Original coordinate: {montage.get_positions()['ch_pos']['LENT 1']}"
 )
 

 

 
Recovered coordinate: [-0.0231477   0.00949445 -0.05183359]
-Original coordinate:  [-0.0231477   0.00949445 -0.05183359]
+Original coordinate: [-0.0231477   0.00949445 -0.05183359]
 

 

 
In summary, as we saw, these standard template spaces that are allowable by
@@ -1676,7 +1492,7 @@ 
Step 5: Store coordinates in a template spaceTotal running time of the script: (0 minutes 36.611 seconds)

+
Total running time of the script: (0 minutes 5.117 seconds)

 

 

@@ -1145,7 +1143,7 @@
 

 

 
This should be very similar to the ds000248 dataset_description.json!

-
Total running time of the script: (0 minutes 5.083 seconds)

+
Total running time of the script: (0 minutes 3.687 seconds)

 

 

@@ -604,17 +604,6 @@ 
Download the data
Using default location ~/mne_data for fnirs_motor_group...
-
-0.00B [00:00, ?B/s]
-5.12kB [00:00, 9.65kB/s]
-5.94MB [00:00, 12.6MB/s]
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-0.00B [00:00, ?B/s]
-0.00B [00:00, ?B/s]
-Download complete in 03s (41.7 MB)
 |fNIRS-motor-group/
 |--- .gitignore
 |--- CITATION.cff
@@ -1134,16 +1123,16 @@ 
Cite mne-bids
readme = op.join(bids_root, "README")
-with open(readme, "r", encoding="utf-8-sig") as fid:
+with open(readme, encoding="utf-8-sig") as fid:
     text = fid.read()
 print(text)
 

 

 
References
 ----------
-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. and Jas, M. (2019). MNE-BIDS: Organizing electrophysiological data into the BIDS format and facilitating their analysis. Journal of Open Source Software 4: (1896). https://doi.org/10.21105/joss.01896
+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. and Jas, M. (2019). MNE-BIDS: Organizing electrophysiological data into the BIDS format and facilitating their analysis. Journal of Open Source Software 4: (1896).https://doi.org/10.21105/joss.01896
 
-In preperation
+Luke, R., Oostenveld, R., Cockx, H., Niso, G., Shader, M., Orihuela-Espina, F., Innes-Brown, H., Tucker, S., Boas, D., Gau, R., Salo, T., Appelhoff, S., Markiewicz, C McAlpine, D., BIDS maintainers, Pollonini, L. (2023). fNIRS-BIDS, the Brain Imaging Data Structure Extended to Functional Near-Infrared Spectroscopy. PsyArXiv. https://doi.org/10.31219/osf.io/7nmcp
 

 

 
Now it’s time to manually check the BIDS directory and the meta files to add
@@ -1154,7 +1143,7 @@ 
Cite mne-bidshttps://bids-standard.github.io/bids-validator/

 
Command line tool: https://www.npmjs.com/package/bids-validator

-
Total running time of the script: (0 minutes 4.002 seconds)

+
Total running time of the script: (0 minutes 0.296 seconds)

 
-
Total running time of the script: (0 minutes 13.893 seconds)

+
Total running time of the script: (0 minutes 10.999 seconds)