Merge pull request #467 from dorahermes/master

HED-SCORE example of EEG and iEEG data with annotations

dataset_listing.tsv

@@ -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

xeeg_hed_score/README

@@ -0,0 +1,29 @@
+# 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]

xeeg_hed_score/dataset_description.json

@@ -0,0 +1,37 @@
+{
+    "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."
+    ]
+}                          

xeeg_hed_score/participants.json

@@ -0,0 +1,6 @@
+{
+  "participant_id": {
+    "LongName": "Participant identifier",
+    "Description": "Unique subject identifier"
+  }
+}

xeeg_hed_score/participants.tsv

@@ -0,0 +1,4 @@
+participant_id
+sub-ieegModulator
+sub-eegArtifactTUH
+sub-eegSeizureTUH

xeeg_hed_score/sub-eegArtifactTUH/ses-eeg01/eeg/sub-eegArtifactTUH_ses-eeg01_task-rest_channels.json

@@ -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."
+	}
+}

xeeg_hed_score/sub-eegArtifactTUH/ses-eeg01/eeg/sub-eegArtifactTUH_ses-eeg01_task-rest_channels.tsv

@@ -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

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

@@ -0,0 +1,9 @@
+{
+	"TaskName": "rest",
+	"TaskDescription": "Subject resting",
+	"InstitutionName": "Temple University Hospital",
+	"EEGReference": "bipolar banana montage",
+	"SamplingFrequency": 250,
+	"PowerLineFrequency": 60,
+	"SoftwareFilters": "n/a"
+}

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

@@ -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/#"
+    }
+}

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

@@ -0,0 +1,15 @@
+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

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

@@ -0,0 +1,9 @@
+{
+	"TaskName": "rest",
+	"TaskDescription": "Subject resting",
+	"InstitutionName": "Temple University Hospital",
+	"EEGReference": "bipolar banana montage",
+	"SamplingFrequency": 250,
+	"PowerLineFrequency": 60,
+	"SoftwareFilters": "n/a"
+}

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

@@ -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/#"
+    }
+}

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

@@ -0,0 +1,5 @@
+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_eeg.json

@@ -0,0 +1,9 @@
+{
+	"TaskName": "rest",
+	"TaskDescription": "Subject resting",
+	"InstitutionName": "Temple University Hospital",
+	"EEGReference": "bipolar banana montage",
+	"SamplingFrequency": 250,
+	"PowerLineFrequency": 60,
+	"SoftwareFilters": "n/a"
+}

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

@@ -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/#"
+    }
+}

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

@@ -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

xeeg_hed_score/sub-eegSeizureTUH/ses-eeg01/eeg/sub-eegSeizureTUH_ses-eeg01_task-rest_channels.json

@@ -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."
+	}
+}

xeeg_hed_score/sub-eegSeizureTUH/ses-eeg01/eeg/sub-eegSeizureTUH_ses-eeg01_task-rest_channels.tsv

@@ -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

xeeg_hed_score/sub-eegSeizureTUH/ses-eeg01/eeg/sub-eegSeizureTUH_ses-eeg01_task-rest_run-000_eeg.json

@@ -0,0 +1,9 @@
+{
+	"TaskName": "rest",
+	"TaskDescription": "Subject resting",
+	"InstitutionName": "Temple University Hospital",
+	"EEGReference": "bipolar banana montage",
+	"SamplingFrequency": 250,
+	"PowerLineFrequency": 60,
+	"SoftwareFilters": "n/a"
+}

xeeg_hed_score/sub-eegSeizureTUH/ses-eeg01/eeg/sub-eegSeizureTUH_ses-eeg01_task-rest_run-001_eeg.json

@@ -0,0 +1,9 @@
+{
+	"TaskName": "rest",
+	"TaskDescription": "Subject resting",
+	"InstitutionName": "Temple University Hospital",
+	"EEGReference": "bipolar banana montage",
+	"SamplingFrequency": 250,
+	"PowerLineFrequency": 60,
+	"SoftwareFilters": "n/a"
+}

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

@@ -0,0 +1,9 @@
+{
+	"TaskName": "rest",
+	"TaskDescription": "Subject resting",
+	"InstitutionName": "Temple University Hospital",
+	"EEGReference": "bipolar banana montage",
+	"SamplingFrequency": 250,
+	"PowerLineFrequency": 60,
+	"SoftwareFilters": "n/a"
+}

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

@@ -0,0 +1,21 @@
+{
+    "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/#"
+    }
+}

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

@@ -0,0 +1,6 @@
+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

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

@@ -0,0 +1,9 @@
+{
+	"TaskName": "rest",
+	"TaskDescription": "Subject resting",
+	"InstitutionName": "Temple University Hospital",
+	"EEGReference": "bipolar banana montage",
+	"SamplingFrequency": 250,
+	"PowerLineFrequency": 60,
+	"SoftwareFilters": "n/a"
+}