EEGdash›OpenNeuro›DS003104
Iss. 3104 · 1 subjects · 1 recordings · CC0
Dataset Brief · MNE-somato-data-bids (anonymized)

DS003104: meg dataset, 1 subjects#

MNE-somato-data-bids (anonymized)

Citation: Lauri Parkkonen, Stefan Appelhoff, Alexandre Gramfort, Mainak Jas, Richard Höchenberger (—). MNE-somato-data-bids (anonymized). 10.18112/openneuro.ds003104.v1.0.1

1-participant MEG dataset — MNE-somato-data-bids (anonymized).

Data & curation Lauri Parkkonen · Stefan Appelhoff · Alexandre Gramfort · Mainak Jas · Richard Höchenberger
MEG · 316 ch300 HzBIDS 1.4.0Task · somatoHealthyTactilePerception
Layer 01Study
What was asked
Hypothesis, independent & dependent variables, paradigm, cohort, and the editorial caveats around what the recordings can and cannot answer.
Layer 02Signal · BIDS
What was recorded
Sidecars, channels & electrodes, coordinate system, event semantics, and quality stats from the NEMAR pipeline when available.
Layer 03Training · ML
What you can train on
Recommended access modes — MNE Raw, braindecode windows, PyTorch DataLoader — plus the targets the metadata makes addressable.
§ 01Access · Get started

Quickstart#

Install

pip install eegdash

Access the data

from eegdash.dataset import DS003104

dataset = DS003104(cache_dir="./data")
# Get the raw object of the first recording
raw = dataset.datasets[0].raw
print(raw.info)

Filter by subject

dataset = DS003104(cache_dir="./data", subject="01")

Advanced query

dataset = DS003104(
    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{ds003104,
  title = {MNE-somato-data-bids (anonymized)},
  author = {Lauri Parkkonen and Stefan Appelhoff and Alexandre Gramfort and Mainak Jas and Richard Höchenberger},
  doi = {10.18112/openneuro.ds003104.v1.0.1},
  url = {https://doi.org/10.18112/openneuro.ds003104.v1.0.1},
}
§ 02Study · The README

About This Dataset#

This dataset contains the MNE-somato-data in BIDS format.

The conversion can be reproduced through the Python script stored in the

/code directory of this dataset. See the README in that directory.

MNE-somato-data-bids

The /derivatives directory contains the outputs of running the FreeSurfer pipeline recon-all on the MRI data with no additional commandline options (only defaults were used): $ recon-all -i sub-01_T1w.nii.gz -s 01 -all After the recon-all call, there were further FreeSurfer calls from the MNE API: $ mne make_scalp_surfaces -s 01 –force $ mne watershed_bem -s 01 The derivatives also contain the forward model *-fwd.fif, which was produced using the source space definition, a *-trans.fif file, and the boundary element model (=conductor model) that lives in freesurfer/subjects/01/bem/*-bem-sol.fif.

The *-trans.fif file is not saved, but can be recovered from the anatomical landmarks in the sub-01/anat/T1w.json file and MNE-BIDS’ function get_head_mri_transform.

See: mne-tools/mne-bids for more information.

Notes on FreeSurfer

the FreeSurfer pipeline recon-all was run new for the sake of converting the somato data to BIDS format. This needed to be done to change the “somato” subject name to the BIDS subject label “01”. Note, that this is NOT “sub-01”, because in BIDS, the “sub-” is just a prefix, whereas the “01” is the subject label.

§ 03Cohort · Participants

Cohort#

Dataset Statistics#

Sex composition

1
subjects
Male
1

Channel counts: 316 ch (n=1 recordings)

Sampling frequencies: 300.3074951171875 Hz (n=1 recordings)

Total recording duration: 14 min

§ 04Signal · Electrodes & trace

Signal · Electrodes & live trace#

Fig. 01 Signal & montage 316 ch · MEG · 300 Hz · 1 subjects, 1 recordings
Live trace viewer — sub-01 · task-somato

Showing one representative recording out of 1 subjects and 1 recordings in this dataset. Browse the full set on OpenNeuro; drop any other _meg.{set,edf,bdf,vhdr} file onto the viewer (or pass ?meg=<url>) to inspect it.

No scalp electrode layout is currently indexed for this dataset. Once the eegdash montage registry ingests it, the interactive viewer will appear here automatically.

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.

NEMAR pipeline statistics — DS003104
HED event descriptors word cloud HED event descriptors word cloud — DS003104
§ 05Manifest · BIDS tree

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.

Recordings—
Files—
Subjects—
Modalities—
Click to load file structure…
Full dataset metadata table

Dataset ID

DS003104

Title

MNE-somato-data-bids (anonymized)

Author (year)

Parkkonen2020

Canonical

—

Importable as

DS003104, Parkkonen2020

Year

—

Authors

Lauri Parkkonen, Stefan Appelhoff, Alexandre Gramfort, Mainak Jas, Richard Höchenberger

License

CC0

Citation / DOI

doi:10.18112/openneuro.ds003104.v1.0.1

Source links

OpenNeuro | NeMAR | Source URL
Copy-paste BibTeX
@dataset{ds003104,
  title = {MNE-somato-data-bids (anonymized)},
  author = {Lauri Parkkonen and Stefan Appelhoff and Alexandre Gramfort and Mainak Jas and Richard Höchenberger},
  doi = {10.18112/openneuro.ds003104.v1.0.1},
  url = {https://doi.org/10.18112/openneuro.ds003104.v1.0.1},
}
§ 06API · Programmatic access

API Reference#

Signature
eegdash.dataset
class
eegdash.dataset.DS003104(cache_dir, query=None, s3_bucket=None, **kwargs)
Bases: EEGDashDataset
Author (year)Parkkonen2020
Canonical—
Importable asDS003104 · Parkkonen2020
Sourceeegdash/dataset/registry.py · [source ↗]
class eegdash.dataset.DS003104(cache_dir: str, query: dict | None = None, s3_bucket: str | None = None, **kwargs)[source]#

MNE-somato-data-bids (anonymized)

Study:

ds003104 (OpenNeuro)

Author (year):

Parkkonen2020

Canonical:

—

Also importable as: DS003104, Parkkonen2020.

Modality: meg; Experiment type: Perception; Subject type: Healthy. Subjects: 1; recordings: 1; 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

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/ds003104 NeMAR dataset: https://nemar.org/dataexplorer/detail?dataset_id=ds003104 DOI: https://doi.org/10.18112/openneuro.ds003104.v1.0.1 NEMAR citation count: 0

Examples

>>> from eegdash.dataset import DS003104
>>> dataset = DS003104(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.

Access modesMNE → braindecode → PyTorch → ML
.rawMNE Raw object — standard tools (filter, epoch, ICA, plot_psd).mne
BaseConcatDatasetEach record is a lazy BaseDataset from braindecode — windowed via create_windows_from_events.braindecode
DataLoaderWraps the windowed dataset into a PyTorch DataLoader; supports parallel workers and on-the-fly augmentations.pytorch
Zarr cacheOptional braindecode Zarr mirror for fast resume; persisted to cache_dir.zarr
Hugging FacePre-bundled mirror at EEGDash/ds003104 · pull with datasets.load_dataset("EEGDash/ds003104").huggingface
Croissant 1.0Machine-readable JSON-LD descriptor — DS003104.croissant.json (MLCommons schema, ingestible by PyTorch / TensorFlow / JAX).mlcommons
Examples using EEGDashcurated · start here
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 ds003104 to reproduce the tutorial on this dataset.

Citation

Lauri Parkkonen, Stefan Appelhoff, Alexandre Gramfort, Mainak Jas, Richard Höchenberger (n.d.). MNE-somato-data-bids (anonymized). 10.18112/openneuro.ds003104.v1.0.1

Provenance

¹Contributed to openneuro in BIDS format.

²Curated & ingested by the EEGDash catalog; see CITATION.cff for canonical reference.

³Persistent identifier: 10.18112/openneuro.ds003104.v1.0.1.

BIDS
BIDS 1.4.0
Sidecars
events · channels · coordsystem
Machine-readable
schema.org/Dataset · Croissant

See Also#