DS002799: ieeg dataset, 27 subjects#

Name: Human es-fMRI Resource: Concurrent deep-brain stimulation and whole-brain functional MRI
License: CC0

Human es-fMRI Resource: Concurrent deep-brain stimulation and whole-brain functional MRI

Access recordings and metadata through EEGDash.

Citation: Thompson WH*, Nair R*, Oya H*, Esteban O, Shine JM, Petkov CI, Poldrack RA, Howard M, Adolphs R†, *equally contributing, †corresponding author (—). Human es-fMRI Resource: Concurrent deep-brain stimulation and whole-brain functional MRI. 10.18112/openneuro.ds002799.v1.0.4

Modality: ieeg Subjects: 27 Recordings: 16824 License: CC0 Source: openneuro

Metadata: Complete (90%)

Quickstart#

Get Started

Install

pip install eegdash

Access the data

from eegdash.dataset import DS002799

dataset = DS002799(cache_dir="./data")
# Get the raw object of the first recording
raw = dataset.datasets[0].raw
print(raw.info)

Query & Filter

Filter by subject

dataset = DS002799(cache_dir="./data", subject="01")

Advanced query

dataset = DS002799(
    cache_dir="./data",
    query={"subject": {"$in": ["01", "02"]}},
)

Iterate recordings

for rec in dataset:
    print(rec.subject, rec.raw.info['sfreq'])

Cite This Dataset

If you use this dataset in your research, please cite the original authors.

BibTeX

@dataset{ds002799,
  title = {Human es-fMRI Resource: Concurrent deep-brain stimulation and whole-brain functional MRI},
  author = {Thompson WH* and Nair R* and Oya H* and Esteban O and Shine JM and Petkov CI and Poldrack RA and Howard M and Adolphs R† and *equally contributing, †corresponding author},
  doi = {10.18112/openneuro.ds002799.v1.0.4},
  url = {https://doi.org/10.18112/openneuro.ds002799.v1.0.4},
}

About This Dataset#

Link to published paper for this data resource: https://rdcu.be/b57kz

This collection contains data from 26 human patients who underwent electrical stimulation during functional magnetic resonance imaging (es-fMRI). The patients had medically refractory epilepsy requiring surgically implanted intracranial electrodes in cortical and subcortical locations. One or multiple contacts on these electrodes were stimulated while simultaneously recording BOLD-fMRI activity in a block design. Multiple runs exist for patients with different stimulation sites. Data is organized in two sessions : Pre-op (pre electrode implantation) and Post-op (post electrode implantation). Raw data is provided in BIDS format and consists of T1s, T2s, resting state scans (pre-op), es-fMRI scans(post-op) , any associated field-maps and stimulation electrode coordinates and stimulation parameters. Pre-processed data (fMRIprep and Freesurfer) is present in the ‘derivatives’ folder.

Notes: 1. Subject IDs 339, 369 and 394 do not have stimulation electrode location data available. 2. Electrodes are in chA-chB format (chA gets leading positive phase of the stimulation). This information is stored in the “channel” file for each stimulation run. 3. In some cases, two distant sites were stimulated simultaneously as indicated by the electrode listed under the appropriate run IDs within the ieeg folders.

Dataset Information#

Dataset ID	`DS002799`
Title	Human es-fMRI Resource: Concurrent deep-brain stimulation and whole-brain functional MRI
Author (year)	`Thompson2024`
Canonical	—
Importable as	`DS002799`, `Thompson2024`
Year	—
Authors	Thompson WH, Nair R, Oya H, Esteban O, Shine JM, Petkov CI, Poldrack RA, Howard M, Adolphs R†, equally contributing, †corresponding author
License	CC0
Citation / DOI	10.18112/openneuro.ds002799.v1.0.4
Source links	OpenNeuro \| NeMAR \| Source URL

Found an issue with this dataset?

If you encounter any problems with this dataset (missing files, incorrect metadata, loading errors, etc.), please let us know!

Report an Issue on GitHub

Technical Details#

Subjects & recordings

Subjects: 27
Recordings: 16824
Tasks: 2

Channels & sampling rate

Channels: 2 (79), 4
Sampling rate (Hz): Varies
Duration (hours): Not calculated

API Reference#

Use the DS002799 class to access this dataset programmatically.

class eegdash.dataset.DS002799(cache_dir: str, query: dict | None = None, s3_bucket: str | None = None, **kwargs)[source]#

Bases: EEGDashDataset

Human es-fMRI Resource: Concurrent deep-brain stimulation and whole-brain functional MRI

Study:: ds002799 (OpenNeuro)
Author (year):: Thompson2024
Canonical:: —

Also importable as: DS002799, Thompson2024.

Modality: ieeg; Experiment type: Clinical/Intervention; Subject type: Epilepsy. Subjects: 27; recordings: 16824; tasks: 2.

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

query#

Merged query with the dataset filter applied.

Type:: dict

records#

Metadata records used to build the dataset, if pre-fetched.

Type:: list[dict] | None

Notes

Each item is a recording; recording-level metadata are available via dataset.description. query supports MongoDB-style filters on fields in ALLOWED_QUERY_FIELDS and is combined with the dataset filter. Dataset-specific caveats are not provided in the summary metadata.

References

OpenNeuro dataset: https://openneuro.org/datasets/ds002799 NeMAR dataset: https://nemar.org/dataexplorer/detail?dataset_id=ds002799 DOI: https://doi.org/10.18112/openneuro.ds002799.v1.0.4

Examples

>>> from eegdash.dataset import DS002799
>>> dataset = DS002799(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, overwrite=False)[source]#

Save the dataset to disk.

Parameters:

path (str or Path) – Destination file path.
overwrite (bool, default False) – If True, overwrite existing file.

Return type:

None