Example of the HED schema library for SCORE implementation

xeeg_hed_score/README

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+# HED schema library for SCORE annotations example
+
+In this work, we developed a HED schema library for the Standardized Computer-based Organized Reporting of EEG (SCORE). Our SCORE implementation in HED tackles the lack of SCORE machine readability and makes it available and machine-readable by open-source software.
+
+This work is related to the (in prep) manuscript:
+Tal Pal Attia et al., (in prep). "Hierarchical Event Descriptor library schema for clinical EEG data annotation".
+
+# General information
+This BIDS project provides examples of the HED SCORE implementation in several EEG and invasive EEG datasets. We included 3 subjects that have:
+- Examples of Modulators.
+- Examples of Seizures.
+- Examples of Artifacts.
+Source data are described below.
+
+## SCORE implementation procedure
+There are two ways to annotate HED in BIDS: by defining an HED column in the _events.tsv or with accompanying _events.json sidecar that lists the HED tags. We provide examples of both.
+ - When annotations are specific to a particular channel, the relevant channel was annotated by including a channel column in the events.tsv file.
+
+# Source data
+ - sub-ieegModulator    Collected at Mayo Clinic Rochester, MN
+ - 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)
+
+# 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: attia.tal@mayo.edu
+Dora Hermes: hermes.dora@mayo.edu

xeeg_hed_score/dataset_description.json

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+{
+    "Name": "HED schema library for SCORE annotations example",
+    "BIDSVersion": "1.7.0",
+    "HEDVersion": "score_1.1.1",
+    "Authors": [
+        "Tal Pal Attia",
+        "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."
+    ]
+}                          

xeeg_hed_score/participants.json

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+{
+  "participant_id": {
+    "LongName": "Participant identifier",
+    "Description": "Unique subject identifier"
+  }
+}

xeeg_hed_score/participants.tsv

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+participant_id
+sub-ieegModulator
+sub-eegArtifactTUH
+sub-eegSeizureTUH

xeeg_hed_score/sub-eegArtifactTUH/ses-eeg01/eeg/sub-eegArtifactTUH_ses-eeg01_channels.json

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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."
+	}
+}

xeeg_hed_score/sub-eegArtifactTUH/ses-eeg01/eeg/sub-eegArtifactTUH_ses-eeg01_channels.tsv

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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

xeeg_hed_score/sub-eegArtifactTUH/ses-eeg01/eeg/sub-eegArtifactTUH_ses-eeg01_task-rest_run-000_events.json

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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": "A spike-like waveform created during patient eye movement. This artifact is usually found on all of the frontal polar electrodes with occasional echoing on the frontal electrodes.",
+            "elec": "An electrode artifact encompasses various electrode related artifacts. Electrode pop is an artifact characterized by channels using the same electrode 'spiking' with an electrographic phase reversal. ",
+            "musc": "Muscle artifact. A very common, high frequency, sharp artifact that corresponds with agitation/nervousness in a patient.",
+            "eyem+musc": "Eye and Muscle"
+        },
+        "HED": {
+            "eyem": "Eye-movement-horizontal-artifact",
+            "elec": "Non-biological-artifact",
+            "musc": "EMG-artifact",
+            "eyem+musc": "(Eye-movement-horizontal-artifact , EMG-artifact)"
+        }
+    },
+    "channel": {
+        "LongName": "Annotated channel",
+        "Description": "Comma-separated list of annotated channels corresponding to *_channels.tsv."
+    }
+}
+
+

xeeg_hed_score/sub-eegArtifactTUH/ses-eeg01/eeg/sub-eegArtifactTUH_ses-eeg01_task-rest_run-000_events.tsv

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+onset	duration	annotation_type	channel
+36.2312	3.5758	eyem	FP1-F7
+91.5725	20.6333	eyem+musc	FP1-F7
+36.2146	3.7334	eyem	FP2-F8
+91.589	20.6416	eyem+musc	FP2-F8
+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
+63.2113	9.9806	elec	C3-CZ,CZ-C4
+91.0913	21.0564	elec	C3-CZ,CZ-C4
+36.4552	3.5177	eyem	FP1-F3
+91.5808	20.5503	eyem+musc	FP1-F3
+36.4054	3.6339	eyem	FP2-F4
+91.5559	20.5752	eyem+musc	FP2-F4

xeeg_hed_score/sub-eegArtifactTUH/ses-eeg01/eeg/sub-eegArtifactTUH_ses-eeg01_task-rest_run-001_events.json

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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": "A spike-like waveform created during patient eye movement. This artifact is usually found on all of the frontal polar electrodes with occasional echoing on the frontal electrodes.",
+            "elec": "An electrode artifact encompasses various electrode related artifacts. Electrode pop is an artifact characterized by channels using the same electrode 'spiking' with an electrographic phase reversal. ",
+            "musc": "Muscle artifact. A very common, high frequency, sharp artifact that corresponds with agitation/nervousness in a patient.",
+            "eyem+musc": "Eye and Muscle"
+        },
+        "HED": {
+            "eyem": "Eye-movement-horizontal-artifact",
+            "elec": "Non-biological-artifact",
+            "musc": "EMG-artifact",
+            "eyem+musc": "(Eye-movement-horizontal-artifact , EMG-artifact)"
+        }
+    },
+    "channel": {
+        "LongName": "Annotated channel",
+        "Description": "Comma-separated list of annotated channels corresponding to *_channels.tsv."
+    }
+}

xeeg_hed_score/sub-eegArtifactTUH/ses-eeg01/eeg/sub-eegArtifactTUH_ses-eeg01_task-rest_run-001_events.tsv

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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

xeeg_hed_score/sub-eegArtifactTUH/ses-eeg01/eeg/sub-eegArtifactTUH_ses-eeg01_task-rest_run-002_events.json

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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": "A spike-like waveform created during patient eye movement. This artifact is usually found on all of the frontal polar electrodes with occasional echoing on the frontal electrodes.",
+            "elec": "An electrode artifact encompasses various electrode related artifacts. Electrode pop is an artifact characterized by channels using the same electrode 'spiking' with an electrographic phase reversal. ",
+            "musc": "Muscle artifact. A very common, high frequency, sharp artifact that corresponds with agitation/nervousness in a patient.",
+            "eyem+musc": "Eye and Muscle"
+        },
+        "HED": {
+            "eyem": "Eye-movement-horizontal-artifact",
+            "elec": "Non-biological-artifact",
+            "musc": "EMG-artifact",
+            "eyem+musc": "(Eye-movement-horizontal-artifact , EMG-artifact)"
+        }
+    },
+    "channel": {
+        "LongName": "Annotated channel",
+        "Description": "Comma-separated list of annotated channels corresponding to *_channels.tsv."
+    }
+}

xeeg_hed_score/sub-eegArtifactTUH/ses-eeg01/eeg/sub-eegArtifactTUH_ses-eeg01_task-rest_run-002_events.tsv

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+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

xeeg_hed_score/sub-eegSeizureTUH/ses-eeg01/eeg/sub-eegSeizureTUH_ses-eeg01_channels.json

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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."
+	}
+}

xeeg_hed_score/sub-eegSeizureTUH/ses-eeg01/eeg/sub-eegSeizureTUH_ses-eeg01_channels.tsv

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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

xeeg_hed_score/sub-eegSeizureTUH/ses-eeg01/eeg/sub-eegSeizureTUH_ses-eeg01_task-rest_run-002_events.json

@@ -0,0 +1,16 @@
+{
+    "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"
+    },
+    "HED_annotations": {
+        "LongName": "Hierarchical Event Descriptors annotations",
+        "Description": "EEG interpretation Hierarchical Event Descriptors annotations"
+    },
+    "channel":{
+        "LongName": "Annotated channel",
+        "Description": "Comma-separated list of annotated channels corresponding to *_channels.tsv."
+    }
+}

xeeg_hed_score/sub-eegSeizureTUH/ses-eeg01/eeg/sub-eegSeizureTUH_ses-eeg01_task-rest_run-002_events.tsv

@@ -0,0 +1,6 @@
+onset	duration	HED_annotations	channel
+24.8325	102.2255	Tonic-clonic-motor-onset-seizure	T3-T5,T5-O1,FP2-F8,T6-O2,A1-T3,T3-C3,C3-CZ,FP1-F3,F3-C3,C3-P3,P3-O1,FP2-F4
+13.8275	159.5516	Tonic-clonic-motor-onset-seizure	F8-T4,T4-T6
+8.8275	118.1255	Tonic-clonic-motor-onset-seizure	CZ-C4,F4-C4,C4-P4,P4-O2
+8.8275	164.3851	Tonic-clonic-motor-onset-seizure	C4-T4
+24.8325	148.4851	Tonic-clonic-motor-onset-seizure	T4-A2

xeeg_hed_score/sub-eegSeizureTUH/ses-eeg01/eeg/sub-eegSeizureTUH_ses-eeg01_task-rest_run-003_events.json

@@ -0,0 +1,16 @@
+{
+    "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"
+    },
+    "HED_annotations": {
+        "LongName": "Hierarchical Event Descriptors annotations",
+        "Description": "EEG interpretation Hierarchical Event Descriptors annotations"
+    },
+    "channel":{
+        "LongName": "Annotated channel",
+        "Description": "Comma-separated list of annotated channels corresponding to *_channels.tsv."
+    }
+}

xeeg_hed_score/sub-eegSeizureTUH/ses-eeg01/eeg/sub-eegSeizureTUH_ses-eeg01_task-rest_run-003_events.tsv

@@ -0,0 +1,9 @@
+onset	duration	HED_annotations	channel
+14.034	101.027	Tonic-clonic-motor-onset-seizure	FP2-F8,T6-O2,A1-T3,T3-C3,C3-CZ
+14.034	160.7442	Tonic-clonic-motor-onset-seizure	F8-T4,T4-T6
+7.9734	107.0876	Tonic-clonic-motor-onset-seizure	CZ-C4
+3.9734	171.532	Tonic-clonic-motor-onset-seizure	C4-T4,T4-A2
+21.2327	93.7906	Tonic-clonic-motor-onset-seizure	FP1-F3,F3-C3,C3-P3,P3-O1,FP2-F4
+3.9623	111.0488	Tonic-clonic-motor-onset-seizure	F4-C4
+13.9334	101.0766	Tonic-clonic-motor-onset-seizure	C4-P4
+3.9789	111.0488	Tonic-clonic-motor-onset-seizure	P4-O2

xeeg_hed_score/sub-eegSeizureTUH/ses-eeg01/eeg/sub-eegSeizureTUH_ses-eeg01_task-rest_run-004_events.json

@@ -0,0 +1,16 @@
+{
+    "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"
+    },
+    "HED_annotations": {
+        "LongName": "Hierarchical Event Descriptors annotations",
+        "Description": "EEG interpretation Hierarchical Event Descriptors annotations"
+    },
+    "channel":{
+        "LongName": "Annotated channel",
+        "Description": "Comma-separated list of annotated channels corresponding to *_channels.tsv."
+    }
+}

xeeg_hed_score/sub-eegSeizureTUH/ses-eeg01/eeg/sub-eegSeizureTUH_ses-eeg01_task-rest_run-004_events.tsv

@@ -0,0 +1,5 @@
+onset	duration	HED_annotations	channel
+26.15	124.3657	Tonic-clonic-motor-onset-seizure	FP2-F8,T6-O2,A1-T3,T3-C3,C3-CZ,FP2-F4
+1	149.5157	Tonic-clonic-motor-onset-seizure	F8-T4,T4-T6,C4-T4,T4-A2
+20.95	129.5657	Tonic-clonic-motor-onset-seizure	CZ-C4,F4-C4,C4-P4,P4-O2
+26.15	76.0424	Tonic-clonic-motor-onset-seizure	FP1-F3,F3-C3,C3-P3,P3-O1

xeeg_hed_score/sub-eegSeizureTUH/ses-eeg01/eeg/sub-eegSeizureTUH_ses-eeg01_task-rest_run-005_events.json

@@ -0,0 +1,16 @@
+{
+    "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"
+    },
+    "HED_annotations": {
+        "LongName": "Hierarchical Event Descriptors annotations",
+        "Description": "EEG interpretation Hierarchical Event Descriptors annotations"
+    },
+    "channel":{
+        "LongName": "Annotated channel",
+        "Description": "Comma-separated list of annotated channels corresponding to *_channels.tsv."
+    }
+}

xeeg_hed_score/sub-eegSeizureTUH/ses-eeg01/eeg/sub-eegSeizureTUH_ses-eeg01_task-rest_run-005_events.tsv

@@ -0,0 +1,5 @@
+onset	duration	HED_annotations	channel
+207.9323	100.0677	Focal-onset-epileptic-seizure	F8-T4
+207.9434	100.0566	Focal-onset-epileptic-seizure	T4-T6
+240.0202	50.2626	Focal-onset-epileptic-seizure	T6-O2
+207.9101	100.0899	Focal-onset-epileptic-seizure	C4-T4,T4-A2

xeeg_hed_score/sub-ieegModulator/ses-ieeg01/ieeg/sub-ieegModulator_ses-ieeg01_coordsystem.json

@@ -0,0 +1,8 @@
+{
+    "IntendedFor": "/sub-ieegModulator/ses-preopMRI/anat/sub-ieegModulator_ses-preopMRI_T1w.nii.gz" ,
+    "iEEGCoordinateSystem": "Other",
+    "iEEGCoordinateUnits": "mm",
+    "iEEGCoordinateSystemDescription": "Native space. The coordinate frame of the scanner at data acquisition of the T1w volume",
+    "iEEGCoordinateProcessingDescription": "sEEG electrode positions from Curry",
+    "iEEGCoordinateProcessingReference": "n/a"
+}