NM000454: ieeg dataset, 15 subjects#
A multimodal epilepsy dataset of paired 3-Tesla and 7-Tesla MRI and intracranial EEG (Penn 3T-7T, Pennsieve 662)
Access recordings and metadata through EEGDash.
Citation: Alfredo Lucas, Mariam Josyula, Nina Petillo, Joost Wagenaar, Joel Stein, Sandhitsu Das, Nishant Sinha, Kathryn Davis, Tamjid Imtiaz (20). A multimodal epilepsy dataset of paired 3-Tesla and 7-Tesla MRI and intracranial EEG (Penn 3T-7T, Pennsieve 662). 10.82901/nemar.nm000454
Modality: ieeg Subjects: 15 Recordings: 1261 License: CC-BY-4.0 Source: nemar
Metadata: Complete (100%)
15-participant iEEG dataset — A multimodal epilepsy dataset of paired 3-Tesla and 7-Tesla MRI and intracranial EEG (Penn 3T-7T, Pennsieve 662).
Quickstart#
Install
pip install eegdash
Access the data
from eegdash.dataset import NM000454
dataset = NM000454(cache_dir="./data")
# Get the raw object of the first recording
raw = dataset.datasets[0].raw
print(raw.info)
Filter by subject
dataset = NM000454(cache_dir="./data", subject="01")
Advanced query
dataset = NM000454(
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{nm000454,
title = {A multimodal epilepsy dataset of paired 3-Tesla and 7-Tesla MRI and intracranial EEG (Penn 3T-7T, Pennsieve 662)},
author = {Alfredo Lucas and Mariam Josyula and Nina Petillo and Joost Wagenaar and Joel Stein and Sandhitsu Das and Nishant Sinha and Kathryn Davis and Tamjid Imtiaz},
doi = {10.82901/nemar.nm000454},
url = {https://doi.org/10.82901/nemar.nm000454},
}
About This Dataset#
Redistribution on NEMAR of Pennsieve Discover dataset 662, version 1 (doi:10.26275/aosz-hj9u, licence CC-BY-4.0),
described in Sci Data 2026, doi:10.1038/s41597-026-07540-5. Authors: Alfredo Lucas, Mariam Josyula, Nina Petillo, Joost Wagenaar, Joel Stein, Sandhitsu Das, Nishant Sinha, Kathryn Davis, Tamjid Imtiaz.
This dataset comprises multimodal paired 3T and 7T MRI scans collected from 30 patients with drug-resistant focal epilepsy along with intracranial EEG data.
A multimodal epilepsy dataset of paired 3-Tesla and 7-Tesla MRI and intracranial EEG
Details (from the paper and the deposit)
c-penn3t7t: Penn 3T-7T Paired Epilepsy Imaging (Pennsieve 662 v1, doi:10.26275/aosz-hj9u)
**Task / paradigm.**30 patients with drug-resistant focal epilepsy with paired 3T and 7T MRI (structural, resting fMRI); for the 15 who later had intracranial EEG, curated ictal and interictal epochs. Ictal epochs from EMU epileptologist notes; interictal epochs randomly selected while awake, >72 h after implantation, >=2 h before seizures and >=2/6/12 h after subclinical/focal/focal-to-bilateral seizures (doi:10.1038/s41597-026-07540-5 (Sci Data 2026, “A multimodal epilepsy dataset of paired 3-Tesla and 7-Tesla MRI and intracranial EEG”, PMC13582879), Methods “Intracranial electroencephalography”). The deposit has 1261 EDF epochs under sourcedata/sub-*/ses-clinical01/ieeg with BIDS channels/events/ieeg.json sidecars.
View full README
A multimodal epilepsy dataset of paired 3-Tesla and 7-Tesla MRI and intracranial EEG
Details (from the paper and the deposit)
c-penn3t7t: Penn 3T-7T Paired Epilepsy Imaging (Pennsieve 662 v1, doi:10.26275/aosz-hj9u)
Task / paradigm.**30 patients with drug-resistant focal epilepsy with paired 3T and 7T MRI (structural, resting fMRI); for the 15 who later had intracranial EEG, curated ictal and interictal epochs. Ictal epochs from EMU epileptologist notes; interictal epochs randomly selected while awake, >72 h after implantation, >=2 h before seizures and >=2/6/12 h after subclinical/focal/focal-to-bilateral seizures (doi:10.1038/s41597-026-07540-5 (Sci Data 2026, “A multimodal epilepsy dataset of paired 3-Tesla and 7-Tesla MRI and intracranial EEG”, PMC13582879), Methods “Intracranial electroencephalography”). The deposit has 1261 EDF epochs under sourcedata/sub-*/ses-clinical01/ieeg with BIDS channels/events/ieeg.json sidecars. **Recording system. Sampling rates 500, 512 or 1024 Hz (paper Methods). Preprocessing described in the paper: 60 Hz notch (Q=30) and 3rd-order Butterworth 1-120 Hz, forward-backward (paper Methods). Amplifier not stated. Reference scheme.**Not stated in the paper text extracted (n/a); see the *_ieeg.json iEEGReference of the deposit. **Electrode types. ECoG grids and strips, SEEG depth electrodes, or both (paper Methods). SEEG contacts in white matter, outside the brain or noisy were excluded from all recordings (paper Methods). Localisation method. Electrodes manually selected on post-implant CT, mapped to the pre-implant MRI with iEEG-recon; atlas assignment (AAL, Lausanne, DKT) per patient (paper Methods “Electrode localization”). The deposit holds, for 15 subjects, iEEG-recon outputs: electrode names, CT voxel, T1 (T00mri) mm/vox and MNI152NLin2009cAsym mm/vox coordinates, and for 12 subjects module3 atlas assignments (DKT antspynet, Atropos tissue, piriform ASHS).
What this BIDS version contains and what was changed
Raw data: the authors’ BIDS tree (deposit
files/sourcedata/) is the root: 30 subjects;ses-research3Tandses-research7T(anat, func resting state),ses-clinical01(iEEG, 15 subjects). Task and run labels of the iEEG epochs (task-ictal<n>/task-interictal<n>, one task label per curated epoch) are kept as released;events.tsvmarks each epochictalorinterictal.iEEG EDF files are the deposit files. Only the EDF header was changed: patient field set to
X X X Xand the day of the start date set to 01 (year, month and clock time kept); the data records are byte-identical (sha256 checked,sourcedata/pennsieve-662-v1/edf_scrub.tsv).The EDFs are not filtered: a 60 Hz line peak is present and power above 120 Hz is kept (spectral check of 40 files), so they are labelled raw (
SoftwareFiltersn/a). The notch and 1-120 Hz band-pass in the paper are its analysis steps._ieeg.json:PowerLineFrequency60 (paper Methods: 60 Hz notch; USA)._channels.tsvunitsfollow the EDF physical dimension of each channel.Electrode positions:
*_space-MNI152NLin2009cAsym_electrodes.tsv(15 subjects) from the deposit’s iEEG-recon outputs (MNI152NLin2009cAsym mm, plus native pre-implant MRI (T00mri) mm columns, DKT/Atropos labels for 12 subjects).region_coarseandatlas_label_aal3_coarseare added by the NEMAR conversion and are derived values.Anatomical MRI: only the images released as defaced are in the BIDS tree;
defacedis part of theacqlabel (acq-3D_defacedbecameacq-3Ddefaced, images without an acq label gotacq-defaced). The MP2RAGE inversion images (inv-1/inv-2) are insourcedata/pennsieve-662-v1/files/sourcedata/with their original names, because their sidecars lackRepetitionTimeExcitation/RepetitionTimePreparation, which BIDS requires and which we do not invent. Head images were checked by eye (sagittal projections) before release. Heudiconv placeholders were removed from sidecars (TaskNameTODO...->rest,CogAtlasIDTODO dropped).Derivatives from the deposit:
derivatives/fmriprep3T,fmriprep7T,freesurfer3T,freesurfer7T,ieeg_recon(same files, regrouped by pipeline).Everything else of the deposit is in
sourcedata/pennsieve-662-v1/with its original relative path (deposit README, manifest, changelog, metadata spreadsheets, clinical CT / pre-implant MRI in iEEG-recon space, electrode voxel files).Calendar dates in text files are set to day 01 (
sourcedata/pennsieve-662-v1/date_scrub.tsv).Not redistributed here (1249 files; list in
sourcedata/pennsieve-662-v1/withheld.tsv): 556 x fMRIPrep report figures/html (slices of the non-defaced T1w); 220 x FreeSurfer whole-head volume computed from non-defaced input (face visible, eye check); 216 x 7T B0 field maps released without defacing (magnitude images show the face); 119 x fMRIPrep preprocessed T1w (whole head; face visible for at least one subject, eye check); 45 x iEEG-recon head image: defacing incomplete for some subjects (eye check); 30 x iEEG-recon registration figure (slices of head MRI/CT); 18 x MP2RAGE UNIT1 image: removal of the face could not be confirmed on the eye check (noise-filled background); inversion images of the same scan are kept; 15 x clinical pre-implant T1w (T00mri): iEEG-recon copies of this scan still show the face for some subjects (eye check); 15 x clinical post-implant CT: facial skeleton/soft tissue not removed (eye check); 9 x FreeSurfer backup transforms (processing timestamp in the file name); 5 x anatomical image not released as defaced; 1 x spreadsheet has date/identifier-like cells or date formats (privacy; participants.tsv carries the clinical columns). They remain available from the original Pennsieve deposit.Missing values are
n/a; nothing was added that the paper or the deposit does not state.
NEMAR Metadata#
[](https://doi.org/10.82901/nemar.nm000454) # A multimodal epilepsy dataset of paired 3-Tesla and 7-Tesla MRI and intracranial EEG Redistribution on NEMAR of Pennsieve Discover dataset 662, version 1 (doi:10.26275/aosz-hj9u, licence CC-BY-4.0), described in Sci Data 2026, doi:10.1038/s41597-026-07540-5. Authors: Alfredo Lucas, Mariam Josyula, Nina Petillo, Joost Wagenaar, Joel Stein, Sandhitsu Das, Nishant Sinha, Kathryn Davis, Tamjid Imtiaz. ## Description from the deposit This dataset comprises multimodal paired 3T and 7T MRI scans collected from 30 patients with drug-resistant focal epilepsy along with intracranial EEG data. ## Details (from the paper and the deposit) # c-penn3t7t: Penn 3T-7T Paired Epilepsy Imaging (Pennsieve 662 v1, doi:10.26275/aosz-hj9u) Task / paradigm. 30 patients with drug-resistant focal epilepsy with paired 3T and 7T MRI (structural, resting fMRI); for the 15 who later had intracranial EEG, curated ictal and interictal epochs. Ictal epochs from EMU epileptologist notes; interictal epochs randomly selected while awake, >72 h after implantation, >=2 h before seizures and >=2/6/12 h after subclinical/focal/focal-to-bilateral seizures (doi:10.1038/s41597-026-07540-5 (Sci Data 2026, “A multimodal epilepsy dataset of paired 3-Tesla and 7-Tesla MRI and intracranial EEG”, PMC13582879), Methods “Intracranial electroencephalography”). The deposit has 1261 EDF epochs under sourcedata/sub-/ses-clinical01/ieeg with BIDS channels/events/ieeg.json sidecars. **Recording system.* Sampling rates 500, 512 or 1024 Hz (paper Methods). Preprocessing described in the paper: 60 Hz notch (Q=30) and 3rd-order Butterworth 1-120 Hz, forward-backward (paper Methods). Amplifier not stated. Reference scheme. Not stated in the paper text extracted (n/a); see the _ieeg.json iEEGReference of the deposit. **Electrode types.* ECoG grids and strips, SEEG depth electrodes, or both (paper Methods). SEEG contacts in white matter, outside the brain or noisy were excluded from all recordings (paper Methods). Localisation method. Electrodes manually selected on post-implant CT, mapped to the pre-implant MRI with iEEG-recon; atlas assignment (AAL, Lausanne, DKT) per patient (paper Methods “Electrode localization”). The deposit holds, for 15 subjects, iEEG-recon outputs: electrode names, CT voxel, T1 (T00mri) mm/vox and MNI152NLin2009cAsym mm/vox coordinates, and for 12 subjects module3 atlas assignments (DKT antspynet, Atropos tissue, piriform ASHS). ## What this BIDS version contains and what was changed - Raw data: the authors’ BIDS tree (deposit files/sourcedata/) is the root: 30 subjects; ses-research3T and
ses-research7T (anat, func resting state), ses-clinical01 (iEEG, 15 subjects). Task and run labels of the iEEG epochs (task-ictal<n> / task-interictal<n>, one task label per curated epoch) are kept as released; events.tsv marks each epoch ictal or interictal.
iEEG EDF files are the deposit files. Only the EDF header was changed: patient field set to X X X X and the day of the start date set to 01 (year, month and clock time kept); the data records are byte-identical (sha256 checked, sourcedata/pennsieve-662-v1/edf_scrub.tsv).
The EDFs are not filtered: a 60 Hz line peak is present and power above 120 Hz is kept (spectral check of 40 files), so they are labelled raw (SoftwareFilters n/a). The notch and 1-120 Hz band-pass in the paper are its analysis steps.
_ieeg.json: PowerLineFrequency 60 (paper Methods: 60 Hz notch; USA). _channels.tsv units follow the EDF physical dimension of each channel.
Electrode positions: *_space-MNI152NLin2009cAsym_electrodes.tsv (15 subjects) from the deposit’s iEEG-recon outputs (MNI152NLin2009cAsym mm, plus native pre-implant MRI (T00mri) mm columns, DKT/Atropos labels for 12 subjects). region_coarse and atlas_label_aal3_coarse are added by the NEMAR conversion and are derived values.
Anatomical MRI: only the images released as defaced are in the BIDS tree; defaced is part of the acq label (acq-3D_defaced became acq-3Ddefaced, images without an acq label got acq-defaced). The MP2RAGE inversion images (inv-1/inv-2) are in sourcedata/pennsieve-662-v1/files/sourcedata/ with their original names, because their sidecars lack RepetitionTimeExcitation/RepetitionTimePreparation, which BIDS requires and which we do not invent. Head images were checked by eye (sagittal projections) before release. Heudiconv placeholders were removed from sidecars (TaskName TODO… -> rest, CogAtlasID TODO dropped).
Derivatives from the deposit: derivatives/fmriprep3T, fmriprep7T, freesurfer3T, freesurfer7T, ieeg_recon (same files, regrouped by pipeline).
Everything else of the deposit is in sourcedata/pennsieve-662-v1/ with its original relative path (deposit README, manifest, changelog, metadata spreadsheets, clinical CT / pre-implant MRI in iEEG-recon space, electrode voxel files).
Calendar dates in text files are set to day 01 (sourcedata/pennsieve-662-v1/date_scrub.tsv).
Not redistributed here (1249 files; list in sourcedata/pennsieve-662-v1/withheld.tsv): 556 x fMRIPrep report figures/html (slices of the non-defaced T1w); 220 x FreeSurfer whole-head volume computed from non-defaced input (face visible, eye check); 216 x 7T B0 field maps released without defacing (magnitude images show the face); 119 x fMRIPrep preprocessed T1w (whole head; face visible for at least one subject, eye check); 45 x iEEG-recon head image: defacing incomplete for some subjects (eye check); 30 x iEEG-recon registration figure (slices of head MRI/CT); 18 x MP2RAGE UNIT1 image: removal of the face could not be confirmed on the eye check (noise-filled background); inversion images of the same scan are kept; 15 x clinical pre-implant T1w (T00mri): iEEG-recon copies of this scan still show the face for some subjects (eye check); 15 x clinical post-implant CT: facial skeleton/soft tissue not removed (eye check); 9 x FreeSurfer backup transforms (processing timestamp in the file name); 5 x anatomical image not released as defaced; 1 x spreadsheet has date/identifier-like cells or date formats (privacy; participants.tsv carries the clinical columns). They remain available from the original Pennsieve deposit.
Missing values are n/a; nothing was added that the paper or the deposit does not state.
License: CC-BY-4.0
Authors:
Alfredo Lucas
Mariam Josyula
Nina Petillo
Joost Wagenaar
Joel Stein
… and 4 more
Versions:
Version |
DOI |
Released |
|---|---|---|
|
Cohort#
Dataset Statistics#
Sex composition
Channel counts (ch)
Sampling frequencies (Hz)
Total recording duration: 27 h
Signal · Electrodes & live trace#
Live trace viewer — sub-PID02 · ses-clinical01 · task-interictal415326 · run-01
Showing one representative recording out of
15 subjects and 1261 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 · 136 sensors — 136 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 |
A multimodal epilepsy dataset of paired 3-Tesla and 7-Tesla MRI and intracranial EEG (Penn 3T-7T, Pennsieve 662) |
Author (year) |
— |
Canonical |
— |
Importable as |
|
Year |
20 |
Authors |
Alfredo Lucas, Mariam Josyula, Nina Petillo, Joost Wagenaar, Joel Stein, Sandhitsu Das, Nishant Sinha, Kathryn Davis, Tamjid Imtiaz |
License |
CC-BY-4.0 |
Citation / DOI |
|
Source links |
OpenNeuro | NeMAR | Source URL |
Copy-paste BibTeX
@dataset{nm000454,
title = {A multimodal epilepsy dataset of paired 3-Tesla and 7-Tesla MRI and intracranial EEG (Penn 3T-7T, Pennsieve 662)},
author = {Alfredo Lucas and Mariam Josyula and Nina Petillo and Joost Wagenaar and Joel Stein and Sandhitsu Das and Nishant Sinha and Kathryn Davis and Tamjid Imtiaz},
doi = {10.82901/nemar.nm000454},
url = {https://doi.org/10.82901/nemar.nm000454},
}
API Reference#
eegdash.datasetEEGDashDataset- class eegdash.dataset.NM000454(cache_dir: str, query: dict | None = None, s3_bucket: str | None = None, **kwargs)[source]#
A multimodal epilepsy dataset of paired 3-Tesla and 7-Tesla MRI and intracranial EEG (Penn 3T-7T, Pennsieve 662)
- Study:
nm000454(NeMAR)- Author (year):
—
- Canonical:
—
Also importable as:
NM000454.Modality:
ieeg; Subject type:Unknown. Subjects: 15; recordings: 1261; tasks: 1255.- 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/nm000454 NeMAR dataset: https://nemar.org/dataexplorer/detail?dataset_id=nm000454 DOI: https://doi.org/10.82901/nemar.nm000454
Examples
>>> from eegdash.dataset import NM000454 >>> dataset = NM000454(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.pytorchSwap any load_dataset(...) call for nm000454 to reproduce the tutorial on this dataset.
Citation
Alfredo Lucas, Mariam Josyula, Nina Petillo, Joost Wagenaar, Joel Stein, … (20). A multimodal epilepsy dataset of paired 3-Tesla and 7-Tesla MRI and intracranial EEG (Penn 3T-7T, Pennsieve 662). 10.82901/nemar.nm000454
Provenance
¹Contributed to nemar in BIDS format.
²Curated & ingested by the EEGDash catalog; see CITATION.cff for canonical reference.
³Persistent identifier: 10.82901/nemar.nm000454.
See Also#
eegdash.dataset.EEGDashDataseteegdash.dataset