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HED-SCORE example of EEG and iEEG data with annotations #467

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1 change: 1 addition & 0 deletions dataset_listing.tsv
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Expand Up @@ -79,3 +79,4 @@ motion_spotrotation participants rotated heading using full-body motion or joyst
mrs_2dmrsi 2D sLASER MRSI data from 8 subjects [link](https://zenodo.org/records/7701228) [@markmikkelsen](https://github.com/markmikkelsen) anat, mrs T1w, mrsi
mrs_biggaba MEGA-PRESS and PRESS MRS data from 12 subjects from one site from the Big GABA project [link](https://www.nitrc.org/projects/biggaba) [@markmikkelsen](https://github.com/markmikkelsen) anat, mrs T1w, mrsref, svs
mrs_fmrs Functional MRS data involving a pain stimulus task from 15 subjects [link](https://www.nitrc.org/projects/fmrs_2020) [@markmikkelsen](https://github.com/markmikkelsen) anat, mrs T1w, events, mrsref, svs
xeeg_hed_score EEG and iEEG data with annotations of artifacts, seizures and modulators using HED-SCORE [@dorahermes](https://github.com/dorahermes) eeg, anat, ieeg channels, coordsystem, electrodes, events, ieeg, eeg, T1w
29 changes: 29 additions & 0 deletions xeeg_hed_score/README
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# BIDS example with HED-SCORE schema library annotations

The HED schema library for the Standardized Computer-based Organized Reporting of EEG (SCORE) can be used to add annotations for BIDS datasets. The annotations are machine readable and validated with the BIDS and HED validators.

The examples are related to the following preprint:
Attia TP, Robbins K, Beniczky S, Bosch-Bayard J, Delorme A, Lundstrom BN, Rogers C, Rampp S, Valdes-Sosa P, Truong D, Worrell G, Makeig S, Hermes D. Hierarchical Event Descriptor library schema for EEG data annotation. arXiv preprint arXiv:2310.15173. 2023 Oct 4.

# General information
This BIDS example set includes 3 subjects where EEG data are annotated according to the HED-SCORE schema library:
- Example subject with annotated Seizures.
- Example subject with annotated Artifacts.
- Example subject with an annotated Modulator (photic stimulation).

Data are annotated by adding a column for annotations in the _events.tsv. This levels/annotations in this column are defined in the _events.json sidecar as HED tags. When annotations are observed in particular EEG channels, the relevant channels is annotated by including a channel column in the events.tsv file.

# Source data
Examples are based on original datasets:
- sub-eegSeizureTUH The TUH EEG Seizure Corpus. Database: TUH EEG Seizure Corpus (TUSZ), Version: 1.5.3, Patient: 258, Session: s003 (../tuh_eeg_seizure/v1.5.3/edf/dev/01_tcp_ar/002/00000258/s003_2003_07_22)
- sub-eegArtifactTUH The TUH EEG Artifact Corpus. Database: TUH EEG Artifact Corpus (TUAR), Version: v2.0.0, Patient: 715 , Session: s010 (../tuh_eeg_artifact/edf/01_tcp_ar/007/00000715/s010_2014_08_07)
- sub-ieegModulator Intracranial EEG dataset collected at Mayo Clinic Rochester, MN during photic stimulation. The photic stimulation is annotated using the HED-SCORE modulator.

# More information
HED: https://www.hedtags.org/
HED schema library for SCORE: https://github.com/hed-standard/hed-schema-library
Temple University Hospital EEG Data Corpus: https://isip.piconepress.com/projects/tuh_eeg/

# Contact
Tal Pal Attia: [email protected]
Dora Hermes: [email protected]
37 changes: 37 additions & 0 deletions xeeg_hed_score/dataset_description.json
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{
"Name": "HED schema library for SCORE annotations example",
"BIDSVersion": "1.9.0",
"HEDVersion": "score_2.0.0",
"Authors": [
"Tal Pal Attia",
"Kay Robbins",
"Dora Hermes"
],
"Acknowledgements": "Kay Robbins, Dung Truong, Arnaud Delorme, and Scott Makeig",
"Funding": [
"National Institute of Health Grant R01MH126700 (SM)",
"National Institute of Health Grant R01MH122258 (DH)"
],
"SourceDatasets": [
{
"Name": "The TUH EEG Seizure Corpus. Database: TUH EEG Seizure Corpus (TUSZ).",
"Version": "1.5.3",
"URL": "https://isip.piconepress.com/projects/tuh_eeg/downloads/"
},
{
"Name": "The TUH EEG Artifact Corpus. Database: TUH EEG Artifact Corpus (TUAR)",
"Version": "2.0.0.",
"URL": "https://isip.piconepress.com/projects/tuh_eeg/downloads/"
}
],
"ReferencesAndLinks": ["https://github.com/hed-standard/hed-schema-library",
"https://www.hedtags.org/",
"Robbins, Kay, Dung Truong, Stefan Appelhoff, Arnaud Delorme, and Scott Makeig. 'Capturing the nature of events and event context using Hierarchical Event Descriptors (HED).' NeuroImage 245 (2021): 118766.",
"Robbins, Kay, Dung Truong, Alexander Jones, Ian Callanan, and Scott Makeig. 'Building FAIR functionality: Annotating events in time series data using Hierarchical Event Descriptors (HED).' Neuroinformatics (2021): 1-19.",
"Obeid, Iyad, and Joseph Picone. 'The temple university hospital EEG data corpus.' Frontiers in neuroscience 10 (2016): 196.",
"Shah, Vinit, Eva Von Weltin, Silvia Lopez, James Riley McHugh, Lillian Veloso, Meysam Golmohammadi, Iyad Obeid, and Joseph Picone. 'The temple university hospital seizure detection corpus.' Frontiers in neuroinformatics 12 (2018): 83.",
"Ochal, Domenic, Safwanur Rahman, Sean Ferrell, Tarek Elseify, Iyad Obeid, and Joseph Picone. 'The temple university hospital eeg corpus: Annotation guidelines.' Institute for Signal and Information Processing Report 1, no. 1 (2020).",
"Buckwalter, G., S. Chhin, S. Rahman, I. Obeid, and J. Picone. 'Recent Advances in the TUH EEG Corpus: Improving the Interrater Agreement for Artifacts and Epileptiform Events.' In 2021 IEEE Signal Processing in Medicine and Biology Symposium (SPMB), pp. 1-3. IEEE, 2021.",
"Hamid, Ahmed, Katherine Gagliano, Safwanur Rahman, Nikita Tulin, Vincent Tchiong, Iyad Obeid, and Joseph Picone. 'The temple university artifact corpus: An annotated corpus of EEG artifacts.' In 2020 IEEE Signal Processing in Medicine and Biology Symposium (SPMB), pp. 1-4. IEEE, 2020."
]
}
6 changes: 6 additions & 0 deletions xeeg_hed_score/participants.json
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{
"participant_id": {
"LongName": "Participant identifier",
"Description": "Unique subject identifier"
}
}
4 changes: 4 additions & 0 deletions xeeg_hed_score/participants.tsv
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participant_id
sub-ieegModulator
sub-eegArtifactTUH
sub-eegSeizureTUH
Empty file.
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{
"name": {
"Description": "REQUIRED. Label of the channel."
},
"type": {
"Description": "REQUIRED. Type of channel; MUST use the channel types listed in bids-specification."
},
"units": {
"Description": "REQUIRED. Physical unit of the value represented in this channel."
}
}
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name type units
FP1-F7 EEG uV
F7-T3 EEG uV
T3-T5 EEG uV
T5-O1 EEG uV
FP2-F8 EEG uV
F8-T4 EEG uV
T4-T6 EEG uV
T6-O2 EEG uV
A1-T3 EEG uV
T3-C3 EEG uV
C3-CZ EEG uV
CZ-C4 EEG uV
C4-T4 EEG uV
T4-A2 EEG uV
FP1-F3 EEG uV
F3-C3 EEG uV
C3-P3 EEG uV
P3-O1 EEG uV
FP2-F4 EEG uV
F4-C4 EEG uV
C4-P4 EEG uV
P4-O2 EEG uV
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{
"TaskName": "rest",
"TaskDescription": "Subject resting",
"InstitutionName": "Temple University Hospital",
"EEGReference": "bipolar banana montage",
"SamplingFrequency": 250,
"PowerLineFrequency": 60,
"SoftwareFilters": "n/a"
}
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{
"onset": {
"Description": "REQUIRED. Onset (in seconds) of the event, measured from the beginning of the acquisition of the first data point stored in the corresponding task data file. Negative onsets are allowed, to account for events that occur prior to the first stored data point."
},
"duration": {
"Description": "REQUIRED. Duration of the event (measured from onset) in seconds"
},
"annotation_type": {
"LongName": "Hierarchical Event Descriptors annotations",
"Description": "EEG interpretation Hierarchical Event Descriptors annotations",
"Levels": {
"eyem": "Eye movements can cause artifacts on recordings. The charge of the eye can especially cause artifacts in electrophysiology data.",
"elec": "Non biological artifacts encompass various electrode related artifacts, such as electrode pop and electrode movement.",
"musc": "EMG artifact. Artifact from muscle activity and myogenic potentials at the measurements site.",
"eyem_musc": "Eye and Muscle artifacts."
},
"HED": {
"eyem": "Eye-movement-artifact",
"elec": "Nonbiological-artifact",
"musc": "EMG-artifact",
"eyem_musc": "(Eye-movement-artifact , EMG-artifact)"
}
},
"channel": {
"LongName": "Annotated channel",
"Description": "Space separated list of annotated channels corresponding to *_channels.tsv.",
"Delimiter": " ",
"HED": "Parameter-value/#"
}
}
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onset duration annotation_type channel
3.9989 2.3064 elec C3-CZ CZ-C4
23.448 2.6466 elec C3-CZ CZ-C4
27.2146 2.9121 elec C3-CZ CZ-C4
31.0476 4.9861 elec C3-CZ CZ-C4
36.2146 3.7334 eyem FP2-F8
36.2312 3.5758 eyem FP1-F7
36.4054 3.6339 eyem FP2-F4
36.4552 3.5177 eyem FP1-F3
63.2113 9.9806 elec C3-CZ CZ-C4
91.0913 21.0564 elec C3-CZ CZ-C4
91.5559 20.5752 eyem_musc FP2-F4
91.5725 20.6333 eyem_musc FP1-F7
91.5808 20.5503 eyem_musc FP1-F3
91.589 20.6416 eyem_musc FP2-F8
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@@ -0,0 +1,9 @@
{
"TaskName": "rest",
"TaskDescription": "Subject resting",
"InstitutionName": "Temple University Hospital",
"EEGReference": "bipolar banana montage",
"SamplingFrequency": 250,
"PowerLineFrequency": 60,
"SoftwareFilters": "n/a"
}
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@@ -0,0 +1,30 @@
{
"onset": {
"Description": "REQUIRED. Onset (in seconds) of the event, measured from the beginning of the acquisition of the first data point stored in the corresponding task data file. Negative onsets are allowed, to account for events that occur prior to the first stored data point."
},
"duration": {
"Description": "REQUIRED. Duration of the event (measured from onset) in seconds"
},
"annotation_type": {
"LongName": "Hierarchical Event Descriptors annotations",
"Description": "EEG interpretation Hierarchical Event Descriptors annotations",
"Levels": {
"eyem": "Eye movements can cause artifacts on recordings. The charge of the eye can especially cause artifacts in electrophysiology data.",
"elec": "Non biological artifacts encompass various electrode related artifacts, such as electrode pop and electrode movement.",
"musc": "EMG artifact. Artifact from muscle activity and myogenic potentials at the measurements site.",
"eyem_musc": "Eye and Muscle artifacts."
},
"HED": {
"eyem": "Eye-movement-artifact",
"elec": "Nonbiological-artifact",
"musc": "EMG-artifact",
"eyem_musc": "(Eye-movement-artifact, EMG-artifact)"
}
},
"channel": {
"LongName": "Annotated channel",
"Description": "Space separated list of annotated channels corresponding to *_channels.tsv.",
"Delimiter": " ",
"HED": "Parameter-value/#"
}
}
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onset duration annotation_type channel
0.531 31.1725 eyem_musc FP1-F7 FP2-F8 FP1-F3 FP2-F4
34.1062 36.1504 eyem_musc FP1-F7 FP2-F8 FP1-F3 FP2-F4
73.1062 22.677 eyem_musc FP1-F7 FP2-F8 FP1-F3 FP2-F4
98.4823 15.0221 eyem FP1-F7 FP2-F8 FP1-F3 FP2-F4
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@@ -0,0 +1,9 @@
{
"TaskName": "rest",
"TaskDescription": "Subject resting",
"InstitutionName": "Temple University Hospital",
"EEGReference": "bipolar banana montage",
"SamplingFrequency": 250,
"PowerLineFrequency": 60,
"SoftwareFilters": "n/a"
}
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@@ -0,0 +1,30 @@
{
"onset": {
"Description": "REQUIRED. Onset (in seconds) of the event, measured from the beginning of the acquisition of the first data point stored in the corresponding task data file. Negative onsets are allowed, to account for events that occur prior to the first stored data point."
},
"duration": {
"Description": "REQUIRED. Duration of the event (measured from onset) in seconds"
},
"annotation_type": {
"LongName": "Hierarchical Event Descriptors annotations",
"Description": "EEG interpretation Hierarchical Event Descriptors annotations",
"Levels": {
"eyem": "Eye movements can cause artifacts on recordings. The charge of the eye can especially cause artifacts in electrophysiology data.",
"elec": "Non biological artifacts encompass various electrode related artifacts, such as electrode pop and electrode movement.",
"musc": "EMG artifact. Artifact from muscle activity and myogenic potentials at the measurements site.",
"eyem_musc": "Eye and Muscle artifacts."
},
"HED": {
"eyem": "Eye-movement-artifact",
"elec": "Nonbiological-artifact",
"musc": "EMG-artifact",
"eyem_musc": "(Eye-movement-artifact, EMG-artifact)"
}
},
"channel": {
"LongName": "Annotated channel",
"Description": "Space separated list of annotated channels corresponding to *_channels.tsv.",
"Delimiter": " ",
"HED": "Parameter-value/#"
}
}
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@@ -0,0 +1,3 @@
onset duration annotation_type channel
0.365 59.3031 eyem_musc FP1-F7 FP2-F8 F8-T4 FP1-F3 FP2-F4
61.0066 5.2489 eyem FP1-F7 FP2-F8 FP1-F3 FP2-F4
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@@ -0,0 +1,11 @@
{
"name": {
"Description": "REQUIRED. Label of the channel."
},
"type": {
"Description": "REQUIRED. Type of channel; MUST use the channel types listed in bids-specification."
},
"units": {
"Description": "REQUIRED. Physical unit of the value represented in this channel."
}
}
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@@ -0,0 +1,23 @@
name type units
FP1-F7 EEG uV
F7-T3 EEG uV
T3-T5 EEG uV
T5-O1 EEG uV
FP2-F8 EEG uV
F8-T4 EEG uV
T4-T6 EEG uV
T6-O2 EEG uV
A1-T3 EEG uV
T3-C3 EEG uV
C3-CZ EEG uV
CZ-C4 EEG uV
C4-T4 EEG uV
T4-A2 EEG uV
FP1-F3 EEG uV
F3-C3 EEG uV
C3-P3 EEG uV
P3-O1 EEG uV
FP2-F4 EEG uV
F4-C4 EEG uV
C4-P4 EEG uV
P4-O2 EEG uV
Original file line number Diff line number Diff line change
@@ -0,0 +1,9 @@
{
"TaskName": "rest",
"TaskDescription": "Subject resting",
"InstitutionName": "Temple University Hospital",
"EEGReference": "bipolar banana montage",
"SamplingFrequency": 250,
"PowerLineFrequency": 60,
"SoftwareFilters": "n/a"
}
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@@ -0,0 +1,9 @@
{
"TaskName": "rest",
"TaskDescription": "Subject resting",
"InstitutionName": "Temple University Hospital",
"EEGReference": "bipolar banana montage",
"SamplingFrequency": 250,
"PowerLineFrequency": 60,
"SoftwareFilters": "n/a"
}
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@@ -0,0 +1,9 @@
{
"TaskName": "rest",
"TaskDescription": "Subject resting",
"InstitutionName": "Temple University Hospital",
"EEGReference": "bipolar banana montage",
"SamplingFrequency": 250,
"PowerLineFrequency": 60,
"SoftwareFilters": "n/a"
}
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{
"duration": {
"HED": "Duration/# second"
},
"seizure_info": {
"LongName": "Hierarchical Event Descriptors annotations",
"Description": "EEG interpretation Hierarchical Event Descriptors annotations from the HED-SCORE library",
"Levels": {
"tcs": "A sequence consisting of a tonic followed by a clonic phase. Definition from ILAE 2017 Classification of Seizure Types Expanded Version."
},
"HED": {
"tcs": "({duration}, (Tonic-clonic-seizure,(Parameter-label/channels,{channel})))"
}
},
"channel":{
"LongName": "Channels involved in the seizure.",
"Description": "Space separated list of annotated channels corresponding to *_channels.tsv.",
"Delimiter": " ",
"HED": "Parameter-value/#"
}
}
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onset duration seizure_info channel
8.8275 118.1255 tcs CZ-C4 F4-C4 C4-P4 P4-O2
8.8275 164.3851 tcs C4-T4
13.8275 159.5516 tcs F8-T4 T4-T6
24.8325 148.4851 tcs T4-A2
24.8325 102.2255 tcs T3-T5 T5-O1 FP2-F8 T6-O2 A1-T3 T3-C3 C3-CZ FP1-F3 F3-C3 C3-P3 P3-O1 FP2-F4
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@@ -0,0 +1,9 @@
{
"TaskName": "rest",
"TaskDescription": "Subject resting",
"InstitutionName": "Temple University Hospital",
"EEGReference": "bipolar banana montage",
"SamplingFrequency": 250,
"PowerLineFrequency": 60,
"SoftwareFilters": "n/a"
}
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