NM000399: ieeg dataset, 11 subjects#
Thalamic local field potentials during reading aloud of words and nonwords (Wang et al., 2022): 11 essential tremor patients, DBS surgery (derivative: preprocessed epochs)
Access recordings and metadata through EEGDash.
Citation: Dengyu Wang, Witold J. Lipski, Alan Bush, Anna Chrabaszcz, Christina Dastolfo-Hromack, Michael W. Dickey, Julie A. Fiez, R. Mark Richardson (2022). Thalamic local field potentials during reading aloud of words and nonwords (Wang et al., 2022): 11 essential tremor patients, DBS surgery (derivative: preprocessed epochs). 10.82901/nemar.nm000399
Modality: ieeg Subjects: 11 Recordings: 26 License: CC0-1.0 Source: nemar
Metadata: Complete (100%)
11-participant iEEG dataset — Thalamic local field potentials during reading aloud of words and nonwords (Wang et al., 2022): 11 essential tremor patients, DBS surgery (derivative: preprocessed epochs).
Quickstart#
Install
pip install eegdash
Access the data
from eegdash.dataset import NM000399
dataset = NM000399(cache_dir="./data")
# Get the raw object of the first recording
raw = dataset.datasets[0].raw
print(raw.info)
Filter by subject
dataset = NM000399(cache_dir="./data", subject="01")
Advanced query
dataset = NM000399(
cache_dir="./data",
query={"subject": {"$in": ["01", "02"]}},
)
Iterate recordings
for rec in dataset:
print(rec.subject, rec.raw.info['sfreq'])
If you use this dataset in your research, please cite the original authors.
BibTeX
@dataset{nm000399,
title = {Thalamic local field potentials during reading aloud of words and nonwords (Wang et al., 2022): 11 essential tremor patients, DBS surgery (derivative: preprocessed epochs)},
author = {Dengyu Wang and Witold J. Lipski and Alan Bush and Anna Chrabaszcz and Christina Dastolfo-Hromack and Michael W. Dickey and Julie A. Fiez and R. Mark Richardson},
doi = {10.82901/nemar.nm000399},
url = {https://doi.org/10.82901/nemar.nm000399},
}
About This Dataset#
Local field potentials from the ventral lateral thalamus of 11 patients with essential tremor during awake DBS
lead implantation (University of Pittsburgh), recorded while they read aloud consonant-vowel-consonant words and nonwords. 4 patients: macroelectrode rings of microelectrode mapping tracks (Alpha Omega Neuro Omega); 7 patients: the implanted DBS lead (Medtronic 3387, Ripple Grapevine), one session after the left lead and one after bilateral implantation. THIS IS A DERIVATIVE DATASET. The Dryad release contains the authors’ preprocessed, epoched signals, not the raw recordings: notch-filtered, resampled to 1 kHz, low-pass 400 Hz, high-pass 2 Hz (field D.state of every file).
doi:10.5061/dryad.zpc866t75 (version 1, 2020-11-02). License: CC0 1.0 (Dryad).
Thalamic LFP during reading aloud of words and nonwords (Wang et al., 2022) - DERIVATIVE
Article: J Neurosci 42(15):3228-3240 (2022), doi:10.1523/JNEUROSCI.1332-21.2022 (PMC8994537); preprint doi:10.1101/2020.07.30.229898. Funding from the Dryad record and article.
All 27 Dryad files were downloaded through the Dryad API and matched the Dryad sha-256 digests and sizes.
Structure of the release and how it is represented
View full README
Thalamic LFP during reading aloud of words and nonwords (Wang et al., 2022) - DERIVATIVE
Article: J Neurosci 42(15):3228-3240 (2022), doi:10.1523/JNEUROSCI.1332-21.2022 (PMC8994537); preprint doi:10.1101/2020.07.30.229898. Funding from the Dryad record and article.
All 27 Dryad files were downloaded through the Dryad API and matched the Dryad sha-256 digests and sizes.
Structure of the release and how it is represented
One file per subject and session (
DBS<id>_session<n>.mat) ->sub-DBS<id>/ses-<n>/ieeg/(subject labels are the release IDs). 26 sessions, 3057 trials.Each trial is stored TWICE in the release:
D.trial{k,1}as preprocessed (no re-referencing) andD.trial{k,2}after common-average re-referencing (rows sum to zero). Only column 1 is converted here. The re-referenced copy is not converted (it is derivable from column 1) and remains in the original files in sourcedata.Trials OVERLAP in time: on the authors’ clock (
D.time) most consecutive trials share samples (2969 of the consecutive trial pairs overlap). A continuous recording cannot be rebuilt from the release. Trials are therefore written back-to-back as segments of one epoched BrainVision file per session (4.86 h of segments in total; the union of the covered time is shorter because of the overlap).events.tsvgives each trial’s segment position, its original start/end time on the authors’ clock, and membership in the authors’ bad-trial lists (badtrial_final, codingbad_idx, quanbad_idx, visobad_idx, partialtrial_idx). No trial was removed.The release has NO per-trial stimulus identity, lexical status (word/nonword) or speech onset/offset; the article states that each session used one of four 120-item lists whose first 60 items alternate words and nonwords and whose last 60 repeat the nonwords, but the list order per session is not released.
Contacts:
macro_a/c/p/m(mapping-track macro rings) ordbs_01..``dbs_08`` (DBS lead contacts; 01-04 left, 05-08 right). Electrode coordinates per session (space-MNI152NLin2009bAsym_electrodes.tsv) come from contact_info.mat (Lead-DBS, MNI ICBM152 NLIN 2009b per the article); matched for 117/117 channel-session pairs.Values: float64 in the release, written as float32 (max absolute error 0.0036 µV, max relative error 5.96e-08).
Participants
Cohort (article): 11 right-handed native English speakers, 3 female, aged 53-84 (median 68), essential tremor. The article’s Table 1 (subject numbers 1-11, not the release IDs): subject 1: 61 M, left, mapping electrodes, 4 sessions; 2: 70 F, right, mapping, 2; 3: 66 M, left, mapping, 2; 4: 75 M, left, mapping, 3; 5: 64 M; 6: 53 M; 7: 67 M; 8: 71 M; 9: 84 F; 10: 73 F; 11: 68 M (5-11: both sides, DBS leads, 2 sessions). The release does not give the correspondence to its DBS<id> codes and the session counts of the mapping-electrode subjects do not match one-to-one, so ages and sexes are not assigned per subject (n/a).
Privacy
Release IDs (DBS4038 …) are research codes. No names or dates in the data; D.time is a time-of-day-like clock in
seconds without a date. MAT-file text-header creation dates in the sourcedata copies are reduced to month and year
(DEIDENTIFICATION_MANIFEST.tsv).
Additional metadata and localisation (added 2026-10-08)
Compiled after the upload from the article, its supplement and the source deposit (each statement names its source). Text and sidecar metadata only; no data file was changed.
Sources: P = Wang et al. 2022, J Neurosci 42(15):3228-3240, doi:10.1523/JNEUROSCI.1332-21.2022 (PMC8994537); D = Dryad doi:10.5061/dryad.zpc866t75 (files read in Voyager Jobs). Recording. 4 subjects: recorded during subcortical mapping with the Neuro Omega system (Alpha Omega). The macroelectrode ring of the mapping electrodes is stainless steel, 0.55 mm in diameter and 1.4 mm long, 3 mm above the tip. Three electrodes ran in a Ben-Gun array (2 mm spacing; anterior/central/posterior or central/posterior/medial trajectories), with up to four sessions at different depths. Sampled at 44 kHz, band-pass 0.075 Hz-10 kHz. 7 subjects: recorded from Medtronic 3387 DBS leads (4 Pt-Ir contacts, 1.27 mm diameter, 1.5 mm long, 1.5 mm spacing) with the Grapevine Neural Interface Processor (Ripple) at 30 kHz. Session 1 was recorded after the left lead was placed (left contacts only), session 2 after bilateral implantation (both leads) (P, “Electrophysiological recordings”). In D, channel labels are macro_a/macro_c/macro_p/macro_m (mapping-electrode trajectories) or dbs_01..dbs_08 (dbs_01-04 left, dbs_05-08 right per contact_info.mat). Reference. The paper’s analysis used a common-average reference (P). The hardware reference is not stated in the paper (n/a). Localisation. Contacts were localised with LEAD-DBS. The post-op scan was coregistered to the pre-op scan with ANTs and normalised to MNI ICBM152 NLIN 2009b, and the electrodes were reconstructed semi-automatically. Contacts were assigned to nuclei of the Ewert et al. 2018 atlas with a 1 mm cut-off: 38/89 sites were in or next to VA/VLa and 51/89 in or next to VLp (P, “Electrode localization”, Results). D/contact_info.mat gives the MNI coordinates of all 89 sites. The per-contact Ewert nucleus labels are not in the deposit.
The column atlas_label_AAL3 of each *_space-MNI152NLin2009bAsym_electrodes.tsv is an AAL3 atlas lookup of the MNI coordinates in that file (ieeg-atlas coord_regions.py, nearest labelled voxel). It is a derived label, not one given by the authors.
NEMAR Metadata#
[](https://doi.org/10.82901/nemar.nm000399) # Thalamic LFP during reading aloud of words and nonwords (Wang et al., 2022) - DERIVATIVE Local field potentials from the ventral lateral thalamus of 11 patients with essential tremor during awake DBS lead implantation (University of Pittsburgh), recorded while they read aloud consonant-vowel-consonant words and nonwords. 4 patients: macroelectrode rings of microelectrode mapping tracks (Alpha Omega Neuro Omega); 7 patients: the implanted DBS lead (Medtronic 3387, Ripple Grapevine), one session after the left lead and one after bilateral implantation. THIS IS A DERIVATIVE DATASET. The Dryad release contains the authors’ preprocessed, epoched signals, not the raw recordings: notch-filtered, resampled to 1 kHz, low-pass 400 Hz, high-pass 2 Hz (field D.state of every file). ## Source - Dryad: Dengyu Wang, Witold J. Lipski, Alan Bush, Anna Chrabaszcz, Christina Dastolfo-Hromack, Michael W. Dickey, Julie A. Fiez, R. Mark Richardson. Thalamic encoding of lexical status is lateralized during reading aloud.
doi:10.5061/dryad.zpc866t75 (version 1, 2020-11-02). License: CC0 1.0 (Dryad).
Article: J Neurosci 42(15):3228-3240 (2022), doi:10.1523/JNEUROSCI.1332-21.2022 (PMC8994537); preprint doi:10.1101/2020.07.30.229898. Funding from the Dryad record and article.
All 27 Dryad files were downloaded through the Dryad API and matched the Dryad sha-256 digests and sizes.
## Structure of the release and how it is represented - One file per subject and session (DBS<id>_session<n>.mat) -> sub-DBS<id>/ses-<n>/ieeg/ (subject labels are the
release IDs). 26 sessions, 3057 trials.
Each trial is stored TWICE in the release: D.trial{k,1} as preprocessed (no re-referencing) and D.trial{k,2} after common-average re-referencing (rows sum to zero). Only column 1 is converted here. The re-referenced copy is not converted (it is derivable from column 1) and remains in the original files in sourcedata.
Trials OVERLAP in time: on the authors’ clock (D.time) most consecutive trials share samples (2969 of the consecutive trial pairs overlap). A continuous recording cannot be rebuilt from the release. Trials are therefore written back-to-back as segments of one epoched BrainVision file per session (4.86 h of segments in total; the union of the covered time is shorter because of the overlap). events.tsv gives each trial’s segment position, its original start/end time on the authors’ clock, and membership in the authors’ bad-trial lists (badtrial_final, codingbad_idx, quanbad_idx, visobad_idx, partialtrial_idx). No trial was removed.
The release has NO per-trial stimulus identity, lexical status (word/nonword) or speech onset/offset; the article states that each session used one of four 120-item lists whose first 60 items alternate words and nonwords and whose last 60 repeat the nonwords, but the list order per session is not released.
Contacts: macro_a/c/p/m (mapping-track macro rings) or dbs_01..`dbs_08` (DBS lead contacts; 01-04 left, 05-08 right). Electrode coordinates per session (space-MNI152NLin2009bAsym_electrodes.tsv) come from contact_info.mat (Lead-DBS, MNI ICBM152 NLIN 2009b per the article); matched for 117/117 channel-session pairs.
Values: float64 in the release, written as float32 (max absolute error 0.0036 µV, max relative error 5.96e-08).
## Participants Cohort (article): 11 right-handed native English speakers, 3 female, aged 53-84 (median 68), essential tremor. The article’s Table 1 (subject numbers 1-11, not the release IDs): subject 1: 61 M, left, mapping electrodes, 4 sessions; 2: 70 F, right, mapping, 2; 3: 66 M, left, mapping, 2; 4: 75 M, left, mapping, 3; 5: 64 M; 6: 53 M; 7: 67 M; 8: 71 M; 9: 84 F; 10: 73 F; 11: 68 M (5-11: both sides, DBS leads, 2 sessions). The release does not give the correspondence to its DBS<id> codes and the session counts of the mapping-electrode subjects do not match one-to-one, so ages and sexes are not assigned per subject (n/a). ## Privacy Release IDs (DBS4038 …) are research codes. No names or dates in the data; D.time is a time-of-day-like clock in seconds without a date. MAT-file text-header creation dates in the sourcedata copies are reduced to month and year (DEIDENTIFICATION_MANIFEST.tsv). ## Additional metadata and localisation (added 2026-10-08) Compiled after the upload from the article, its supplement and the source deposit (each statement names its source). Text and sidecar metadata only; no data file was changed. Sources: P = Wang et al. 2022, J Neurosci 42(15):3228-3240, doi:10.1523/JNEUROSCI.1332-21.2022 (PMC8994537); D = Dryad doi:10.5061/dryad.zpc866t75 (files read in Voyager Jobs). Recording. 4 subjects: recorded during subcortical mapping with the Neuro Omega system (Alpha Omega). The macroelectrode ring of the mapping electrodes is stainless steel, 0.55 mm in diameter and 1.4 mm long, 3 mm above the tip. Three electrodes ran in a Ben-Gun array (2 mm spacing; anterior/central/posterior or central/posterior/medial trajectories), with up to four sessions at different depths. Sampled at 44 kHz, band-pass 0.075 Hz-10 kHz. 7 subjects: recorded from Medtronic 3387 DBS leads (4 Pt-Ir contacts, 1.27 mm diameter, 1.5 mm long, 1.5 mm spacing) with the Grapevine Neural Interface Processor (Ripple) at 30 kHz. Session 1 was recorded after the left lead was placed (left contacts only), session 2 after bilateral implantation (both leads) (P, “Electrophysiological recordings”). In D, channel labels are macro_a/macro_c/macro_p/macro_m (mapping-electrode trajectories) or dbs_01..dbs_08 (dbs_01-04 left, dbs_05-08 right per contact_info.mat). Reference. The paper’s analysis used a common-average reference (P). The hardware reference is not stated in the paper (n/a). Localisation. Contacts were localised with LEAD-DBS. The post-op scan was coregistered to the pre-op scan with ANTs and normalised to MNI ICBM152 NLIN 2009b, and the electrodes were reconstructed semi-automatically. Contacts were assigned to nuclei of the Ewert et al. 2018 atlas with a 1 mm cut-off: 38/89 sites were in or next to VA/VLa and 51/89 in or next to VLp (P, “Electrode localization”, Results). D/contact_info.mat gives the MNI coordinates of all 89 sites. The per-contact Ewert nucleus labels are not in the deposit. The column atlas_label_AAL3 of each *_space-MNI152NLin2009bAsym_electrodes.tsv is an AAL3 atlas lookup of the MNI coordinates in that file (ieeg-atlas coord_regions.py, nearest labelled voxel). It is a derived label, not one given by the authors.
License: CC0-1.0
Authors:
Dengyu Wang
Witold J. Lipski
Alan Bush
Anna Chrabaszcz
Christina Dastolfo-Hromack
… and 3 more
Versions:
Version |
DOI |
Released |
|---|---|---|
|
Cohort#
Dataset Statistics#
Channel counts (ch)
Sampling frequencies: 1000.0 Hz (n=26 recordings)
Total recording duration: 4 h 51 min
Signal · Electrodes & live trace#
Live trace viewer — sub-DBS4038 · ses-2 · task-reading
Showing one representative recording out of
11 subjects and 26 recordings in this dataset.
Browse the full set on OpenNeuro;
drop any other _ieeg.{set,edf,bdf,vhdr} file onto the
viewer (or pass ?ieeg=<url>) to inspect it.
Electrode layout — iEEG · 8 sensors — 8 channels
NEMAR Processing Statistics#
The plots below are generated by NEMAR’s automated EEG pipeline. The histogram shows pipeline success for data cleaning and ICA decomposition, the percentage of data frames and EEG channels retained after artefact removal, line noise per channel (RMS, dB), and the age/gender distribution of participants.
HED event descriptors word cloud
Manifest#
File Explorer#
Browse the BIDS file structure of this dataset. Records are fetched on demand from the EEGDash catalog the first time you open the explorer.
Full dataset metadata table
Dataset ID |
|
Title |
Thalamic local field potentials during reading aloud of words and nonwords (Wang et al., 2022): 11 essential tremor patients, DBS surgery (derivative: preprocessed epochs) |
Author (year) |
— |
Canonical |
— |
Importable as |
|
Year |
2022 |
Authors |
Dengyu Wang, Witold J. Lipski, Alan Bush, Anna Chrabaszcz, Christina Dastolfo-Hromack, Michael W. Dickey, Julie A. Fiez, R. Mark Richardson |
License |
CC0-1.0 |
Citation / DOI |
|
Source links |
OpenNeuro | NeMAR | Source URL |
Copy-paste BibTeX
@dataset{nm000399,
title = {Thalamic local field potentials during reading aloud of words and nonwords (Wang et al., 2022): 11 essential tremor patients, DBS surgery (derivative: preprocessed epochs)},
author = {Dengyu Wang and Witold J. Lipski and Alan Bush and Anna Chrabaszcz and Christina Dastolfo-Hromack and Michael W. Dickey and Julie A. Fiez and R. Mark Richardson},
doi = {10.82901/nemar.nm000399},
url = {https://doi.org/10.82901/nemar.nm000399},
}
API Reference#
eegdash.datasetEEGDashDataset- class eegdash.dataset.NM000399(cache_dir: str, query: dict | None = None, s3_bucket: str | None = None, **kwargs)[source]#
Thalamic local field potentials during reading aloud of words and nonwords (Wang et al., 2022): 11 essential tremor patients, DBS surgery (derivative: preprocessed epochs)
- Study:
nm000399(NeMAR)- Author (year):
—
- Canonical:
—
Also importable as:
NM000399.Modality:
ieeg; Subject type:Unknown. Subjects: 11; recordings: 26; tasks: 1.- Parameters:
cache_dir (str | Path) – Directory where data are cached locally.
query (dict | None) – Additional MongoDB-style filters to AND with the dataset selection. Must not contain the key
dataset.s3_bucket (str | None) – Base S3 bucket used to locate the data.
**kwargs (dict) – Additional keyword arguments forwarded to
EEGDashDataset.
- data_dir#
Local dataset cache directory (
cache_dir / dataset_id).- Type:
Path
Notes
Each item is a recording; recording-level metadata are available via
dataset.description.querysupports MongoDB-style filters on fields inALLOWED_QUERY_FIELDSand is combined with the dataset filter. Dataset-specific caveats are not provided in the summary metadata.References
OpenNeuro dataset: https://openneuro.org/datasets/nm000399 NeMAR dataset: https://nemar.org/dataexplorer/detail?dataset_id=nm000399 DOI: https://doi.org/10.82901/nemar.nm000399
Examples
>>> from eegdash.dataset import NM000399 >>> dataset = NM000399(cache_dir="./data") >>> recording = dataset[0] >>> raw = recording.load()
- __init__(cache_dir: str, query: dict | None = None, s3_bucket: str | None = None, **kwargs)[source]#
- save(path: str, overwrite: bool = False, offset: int = 0)[source]#
Save datasets to files by creating one subdirectory for each dataset:
path/ 0/ 0-raw.fif | 0-epo.fif description.json raw_preproc_kwargs.json (if raws were preprocessed) window_kwargs.json (if this is a windowed dataset) window_preproc_kwargs.json (if windows were preprocessed) target_name.json (if target_name is not None and dataset is raw) 1/ 1-raw.fif | 1-epo.fif description.json raw_preproc_kwargs.json (if raws were preprocessed) window_kwargs.json (if this is a windowed dataset) window_preproc_kwargs.json (if windows were preprocessed) target_name.json (if target_name is not None and dataset is raw)
- Parameters:
path (str) –
- Directory in which subdirectories are created to store
-raw.fif | -epo.fif and .json files to.
overwrite (bool) – Whether to delete old subdirectories that will be saved to in this call.
offset (int) – If provided, the integer is added to the id of the dataset in the concat. This is useful in the setting of very large datasets, where one dataset has to be processed and saved at a time to account for its original position.
BaseDataset from braindecode — windowed via create_windows_from_events.braindecodeDataLoader; supports parallel workers and on-the-fly augmentations.pytorch
Find datasets with the EEGDash APIQuery the catalogue, filter by task or modality, list candidates.
Load one EEG recordingResolve a single record to an MNE Raw with channels and events.
EEG recording to PyTorch DataLoaderWrap braindecode windows in a DataLoader for model training.
Preprocess EEG and create windowsFilter, resample, epoch — and persist the windowed dataset.
Save and reload prepared dataCache a windowed dataset to disk and reattach it without recompute.
Download a dataset locallyPrefetch BIDS files to a local cache and validate the layout.Swap any load_dataset(...) call for nm000399 to reproduce the tutorial on this dataset.
Citation
Dengyu Wang, Witold J. Lipski, Alan Bush, Anna Chrabaszcz, Christina Dastolfo-Hromack, … (2022). Thalamic local field potentials during reading aloud of words and nonwords (Wang et al., 2022): 11 essential tremor patients, DBS surgery (derivative: preprocessed epochs). 10.82901/nemar.nm000399
Provenance
¹Contributed to nemar in BIDS format.
²Curated & ingested by the EEGDash catalog; see CITATION.cff for canonical reference.
³Persistent identifier: 10.82901/nemar.nm000399.
See Also#
eegdash.dataset.EEGDashDataseteegdash.dataset