From 0911c3a36db5a5a605595c84df033ab6274ee0d9 Mon Sep 17 00:00:00 2001 From: "Yaroslav O. Halchenko" Date: Tue, 6 May 2025 17:52:13 -0400 Subject: [PATCH] Add .nwb as supported format for EEG NWB is BRAIN Initiative supported, and open data standard https://neurodatawithoutborders.github.io/ . The main motivation here is to support joint iEEG and EEG datasets for EMBER archive project. Quick google can show that there is a good number of studies which have conjoint EEG and iEEG. Since .nwb is supported for iEEG, it makes only sense to add support for it in EEG modality as well. There is a good number of .nwb "specific" tools in the ecosystem, with a notable mention of https://neurosift.app which allows "smart" client-side (in browser) access to remote .nwb files for exploration. It seems that there is also growing number of toolkits in EEG world which support NWB. E.g., EEGLAB already input support for NWB: https://eeglab.org/plugins/NWB-io/ so data would be accessible in this popular toolkit. Added listing of NWB into EEG formats table + harmonize (change URL also) in iEEG section --- src/modality-specific-files/electroencephalography.md | 2 ++ .../intracranial-electroencephalography.md | 3 ++- src/schema/rules/files/raw/eeg.yaml | 1 + 3 files changed, 5 insertions(+), 1 deletion(-) diff --git a/src/modality-specific-files/electroencephalography.md b/src/modality-specific-files/electroencephalography.md index cb765c9549..52dcbd6cd7 100644 --- a/src/modality-specific-files/electroencephalography.md +++ b/src/modality-specific-files/electroencephalography.md @@ -37,6 +37,7 @@ stored in one of the following formats: | [BrainVision Core Data Format][bvformat] | `.vhdr`, `.vmrk`, `.eeg` | Each recording consists of a `.vhdr`, `.vmrk`, `.eeg` file triplet. | | [EEGLAB](https://sccn.ucsd.edu/eeglab/index.php) | `.set`, `.fdt` | The format used by the MATLAB toolbox [EEGLAB](https://sccn.ucsd.edu/eeglab/index.php). Each recording consists of a `.set` file with an OPTIONAL `.fdt` file. | | [Biosemi](https://www.biosemi.com/) | `.bdf` | Each recording consists of a single `.bdf` file. [`bdf+`](https://www.teuniz.net/edfbrowser/bdfplus%20format%20description.html) files are permitted. The capital `.BDF` extension MUST NOT be used. | +| [Neurodata Without Borders (NWB)][nwb] | `.nwb` | Each recording consists of a single `.nwb` file. | It is RECOMMENDED to use the European data format, or the BrainVision data format. It is furthermore discouraged to use the other accepted formats over @@ -490,3 +491,4 @@ actual anatomical nasion: `sub-0001_ses-001_acq-NAS_photo.jpg` [bvformat]: https://www.brainproducts.com/support-resources/brainvision-core-data-format-1-0/ +[nwb]: https://neurodatawithoutborders.github.io/ diff --git a/src/modality-specific-files/intracranial-electroencephalography.md b/src/modality-specific-files/intracranial-electroencephalography.md index 1d5e146383..0df232221b 100644 --- a/src/modality-specific-files/intracranial-electroencephalography.md +++ b/src/modality-specific-files/intracranial-electroencephalography.md @@ -36,7 +36,7 @@ stored in one of the following formats: | [European data format](https://www.edfplus.info/) | `.edf` | Each recording consists of a `.edf` single file. [`edf+`](https://www.edfplus.info/specs/edfplus.html) files are permitted. The capital `.EDF` extension MUST NOT be used. | | [BrainVision Core Data Format][bvformat] | `.vhdr`, `.vmrk`, `.eeg` | Each recording consists of a `.vhdr`, `.vmrk`, `.eeg` file triplet. | | [EEGLAB](https://sccn.ucsd.edu/eeglab/index.php) | `.set`, `.fdt` | The format used by the MATLAB toolbox [EEGLAB](https://sccn.ucsd.edu/eeglab/index.php). Each recording consists of a `.set` file with an OPTIONAL `.fdt` file. | -| [Neurodata Without Borders](https://nwb-schema.readthedocs.io/en/latest/) | `.nwb` | Each recording consists of a single `.nwb` file. | +| [Neurodata Without Borders][nwb] | `.nwb` | Each recording consists of a single `.nwb` file. | | [MEF3](https://osf.io/e3sf9/) | `.mefd` | Each recording consists of a `.mefd` directory. | | [MED](https://medformat.org/) | `.medd` | Each recording consists of a `.medd` directory. | @@ -547,3 +547,4 @@ onset duration trial_type electrical_stimulation_type electrical_stimulation_sit [bvformat]: https://www.brainproducts.com/support-resources/brainvision-core-data-format-1-0/ +[nwb]: https://neurodatawithoutborders.github.io/ diff --git a/src/schema/rules/files/raw/eeg.yaml b/src/schema/rules/files/raw/eeg.yaml index 676d66dc1b..c0b81be8b8 100644 --- a/src/schema/rules/files/raw/eeg.yaml +++ b/src/schema/rules/files/raw/eeg.yaml @@ -11,6 +11,7 @@ eeg: - .set - .fdt - .bdf + - .nwb datatypes: - eeg entities: