[WIP] BEP042 - Emg examples

emg_examples/.bidsignore

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+# Ignore any markdown file in the root directory, they include the source specifications
+*.md

emg_examples/README.md

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+# EMG BIDS Examples Dataset
+
+This dataset contains examples of different EMG recording setups to demonstrate various ways of documenting EMG data according to the BIDS specification. Each example includes metadata files in BIDS format describing the recording setup, electrode placement, and other relevant information. The examples follow a discussion of the [EMG metadata fields](https://docs.google.com/document/d/1s4SbStsm2VXqFbHEVF6Og7BCtjsRUDhzcZj9LO07r6Q) during the development of the BIDS-EMG extension. Each subject represents a different EMG recording configuration, showcasing different aspects of EMG metadata documentation.
+
+## Dataset Structure
+
+The dataset includes 6 example subjects showing different EMG recording configurations:
+
+```shell
+.
+├── dataset_description.json
+├── participants.json 
+├── participants.tsv
+├── sub-s1CustomBipolar/
+├── sub-s2IndependentMod/
+├── sub-s3CustomBipolarFace/
+├── sub-s5TwoHDsEMG/
+├── sub-s6MutliBodyParts/
+└── sub-s8concurrentIndepndentUnits/
+```
+
+## Example Descriptions
+
+### sub-s1CustomBipolar
+Demonstrates documentation of a custom-made bipolar EMG system recording from flexors of the lower arm. Shows how to document:
+- Single channel bipolar montage
+- Precise electrode placement using anatomical landmarks
+- Inter-electrode distance specifications
+
+### sub-s2IndependentMod 
+Shows documentation for commercial bipolar EMG modules recording from multiple muscles. Highlights:
+- Multiple independent bipolar channels
+- Wireless sensors
+- Documentation of multiple target muscles
+
+### sub-s3CustomBipolarFace
+Illustrates recording from facial muscles with:
+- Many-to-many mapping between sensors and muscles
+- Functional localization for electrode placement
+- Recording from muscles without bony landmarks
+
+### sub-s5TwoHDsEMG
+Demonstrates high-density EMG grid recordings from two body parts:
+- Multiple HD-EMG grids
+- Grid placement documentation
+- Channel grouping specifications
+
+### sub-s6MutliBodyParts
+Shows recording from multiple body parts with:
+- Different types of electrodes
+- Multiple amplifier configurations
+- Complex electrode placement schemes
+
+### sub-s8concurrentIndepndentUnits
+Illustrates concurrent recording with:
+- Multiple independent recording units
+- Different sampling rates
+- Synchronization between units
+
+## Purpose
+
+This dataset serves as a reference implementation showing how different EMG recording setups can be documented in BIDS format. Each example demonstrates specific aspects of EMG metadata documentation including:
+
+- Electrode placement methods
+- Montage types
+- Channel configurations
+- Target muscle documentation
+- Recording system specifications
+- Spatial relationships between electrodes
+
+## Usage
+
+These examples can be used as templates when converting EMG data to BIDS format. The metadata fields and documentation approaches shown here cover common EMG recording scenarios.

emg_examples/dataset_description.json

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+{
+  "Name": "Sample EMG dataset",
+  "License": "BSD 3-Clause",
+  "Authors": ["BEP042 Team"], 
+  "ReferencesAndLinks": ["https://github.com/bids-standard/bids-specification/issues/1371",
+                          "https://github.com/bids-standard/bids-specification/pull/1998"],
+  "EthicsApprovals": ["Datasets are de-identified hypotheticals and do not require ethics approval."],
+  "BIDSVersion": "1.10.0",
+  "HEDVersion": "8.3.0",
+  "DatasetType": "raw",
+  "Acknowledgements": "We thank the participants and their families for their time and effort. We also thank the NeuroScience Gateway team for providing computational resources.",
+  "GeneratedBy":[ {
+    "Name": "bids-matlab-tools",
+    "Version": "9.1"
+  }]
+}

emg_examples/participants.json

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+{
+  "participant_id": {
+    "Description": "The prticipant name corresponding to the examples in the metadata discussion"
+  },
+  "sex": {
+    "LongName": "Gender",
+    "Description": "Gender",
+    "Levels": {
+      "F": "Female",
+      "M": "Male"
+    }
+  },
+  "age": {
+    "LongName": "Age",
+    "Description": "Age in years"
+  }
+}

emg_examples/participants.tsv

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+participant_id	age sex
+sub-s1CustomBipolar	25	M
+sub-s2IndependentMod	30	F
+sub-s3CustomBipolarFace	35	M
+sub-s5TwoHDsEMG	40	F
+sub-s6MutliBodyParts	45	M
+sub-s8concurrentIndepndentUnits	50	F
+sub-s9TwoWristbands    55	M

emg_examples/sub-s1CustomBipolar/emg/sub-s1CustomBipolar_task-holdWeight_channels.tsv

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+name	type	units	reference	interelectrode_distance	target_muscle
+EMG1	emg	V	bipolar	20 mm	Flexor carpi radialis, Pronator teres, Brachioradialis

emg_examples/sub-s1CustomBipolar/emg/sub-s1CustomBipolar_task-holdWeight_emg.json

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+{
+	"EMGChannelCount":1,
+	"EMGPlacementScheme":"Center of electrode pair placed at 50% on the line between the posterior crista of the acromion and the olecranon, 2 finger widths lateral.",
+	"EMGReference":"bipolar",
+	"EMGGround":"Medial bony landmark of the elbow",
+    "EMGElectrodeCount":3,
+    "ElectrodeMaterial":"Ag/AgCl",
+	"Manufacturer":"Custom",
+	"ManufacturersModelName":"Raspberry Pi",
+    "AmpifierType":"Wired",
+	"RecordingDuration":1.00,
+	"SamplingFrequency":2000,
+	"TaskDescription":"The subject was holding an object with differnt weights for 5 seconds.",
+	"TaskName":"holdWeight",
+	"TriggerChannelCount":0
+}

emg_examples/sub-s2IndependentMod/emg/sub-s2IndependentMod_task-grasping_channels.tsv

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+name	type	units	target_muscle	interelectrode_distance	placement
+EMG1	emg	V	Flexor carpi radialis	20 mm	near the elbow crease on the inner forearm
+EMG2	emg	V	Extensor radialis brevis	20 mm	dorsal side of the forearm, about halfway between the elbow and the wrist
+EMG3	emg	V	Brachioradialis	20 mm	upper forearm, about one-third of the way down from the elbow, on the lateral side
+EMG4	emg	V	Flexor digitorum superficialis	20 mm	Locate the midpoint of the inner forearm
+EMG5	emg	V	Flexor carpi ulnaris	20 mm	above the wrist on the inner forearm
+EMG6	emg	V	Abductor pollicis brevis	20 mm	Over the fleshy area at the base of the thumb

emg_examples/sub-s2IndependentMod/emg/sub-s2IndependentMod_task-grasping_emg.json

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+{
+	"EMGChannelCount":6,
+	"EMGPlacementScheme":"Electrodes placed on lower arm and hand muscles; see channels.tsv for details.",
+	"EMGReference":"bipolar",
+	"EMGGround":"n/a",
+    "EMGElectrodeCount":12,
+    "ElectrodeMaterial":"Ag/AgCl",
+	"Manufacturer":"Cometa",
+	"ManufacturersModelName":"MiniX",
+    "AmpifierType":"Wireless",
+	"RecordingDuration":1.00,
+	"SamplingFrequency":2000,
+    "HardwareFilters":"loawpass at 500 Hz",
+	"TaskDescription":"Subject reaches out to grasp an object with different weights for 5 seconds.",
+	"TaskName":"grasping",
+	"TriggerChannelCount":0
+}

emg_examples/sub-s3CustomBipolarFace/emg/sub-s3CustomBipolarFace_task-talking_channels.tsv

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+name	type	units	reference	target_muscle	interelectrode_distance	signal_electrode
+EMG1	emg	V	E2	tongue, anterior belly of the digastric	n/a	E1
+EMG2	emg	V	E4	levator angulis oris, zygomaticus major	20 mm	E3
+EMG3	emg	V	E6	levator angulis oris, zygomaticus major	n/a	E5
+EMG4	emg	V	E8	platysma	n/a	E7
+EMG5	emg	V	E10	orbicularis oris	n/a	E9
+EMG6	emg	V	E12	tongue	20 mm	E11

emg_examples/sub-s3CustomBipolarFace/emg/sub-s3CustomBipolarFace_task-talking_electrodes.json

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+{
+    "Coordsystem": {
+        "EMGCoordinateUnits": "percent",
+        "EMGCoordinateSystemDescription": "X: LHJ → RHJ; Y: Inion → Nasion; Z: MMP → Vertex; Left Helix-Tragus Junction; (LHJ) Right Helix-Tragus Junction(RHJ); Vertex Midpoint between Mastoid processs(MMP)"
+    }
+}

emg_examples/sub-s3CustomBipolarFace/emg/sub-s3CustomBipolarFace_task-talking_electrodes.tsv

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+name	x	y	z
+E1	20	80	0
+E2	40	100	50
+E3	10	90	40
+E4	20	90	40
+E5	70	90	40
+E6	0	50	30
+E7	80	90	30
+E8	100	50	30
+E9	50	100	20
+E10	100	50	30
+E11	60	60	-10
+E12	70	60	-10

emg_examples/sub-s3CustomBipolarFace/emg/sub-s3CustomBipolarFace_task-talking_emg.json

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+{
+	"EMGChannelCount":6,
+	"EMGPlacementScheme":"Electrodes placed over articulatory muscles on the lower face.",
+	"EMGReference":"Behind the ear (Mastoid)",
+	"EMGGround":"n/a",
+    "EMGElectrodeCount":13,
+    "ElectrodeMaterial":"Ag/AgCl",
+	"Manufacturer":"Custom",
+	"ManufacturersModelName":"n/a",
+    "AmpifierType":"Wired",
+	"RecordingDuration":1.00,
+	"SamplingFrequency":2000,
+	"TaskDescription":"Subject perofrmed speech tasks.",
+	"TaskName":"talking",
+	"TriggerChannelCount":0
+}

emg_examples/sub-s5TwoHDsEMG/emg/sub-s5TwoHDsEMG_task-isometric_channels.tsv

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+name	type	units	reference	target_muscle	group	signal_electrode
+EMG1	emg	V	R1	forearm flexors	Grid1	E1
+EMG2	emg	V	R1	forearm flexors	Grid1	E2
+EMG3	emg	V	R1	forearm flexors	Grid1	E3
+EMG4	emg	V	R1	forearm flexors	Grid1	E4
+EMG5	emg	V	R1	forearm flexors	Grid1	E5
+EMG6	emg	V	R1	forearm flexors	Grid1	E6
+EMG7	emg	V	R1	forearm flexors	Grid1	E7
+EMG8	emg	V	R1	forearm flexors	Grid1	E8
+EMG9	emg	V	R1	forearm flexors	Grid1	E9
+EMG10	emg	V	R1	forearm flexors	Grid1	E10
+EMG11	emg	V	R1	forearm flexors	Grid1	E11
+EMG12	emg	V	R1	forearm flexors	Grid1	E12
+EMG13	emg	V	R1	forearm flexors	Grid1	E13
+EMG14	emg	V	R1	forearm flexors	Grid1	E14
+EMG15	emg	V	R1	forearm flexors	Grid1	E15
+EMG16	emg	V	R1	forearm flexors	Grid1	E16
+EMG17	emg	V	R1	forearm flexors	Grid1	E17
+EMG18	emg	V	R1	forearm flexors	Grid1	E18
+EMG19	emg	V	R1	forearm flexors	Grid1	E19
+EMG20	emg	V	R1	forearm flexors	Grid1	E20
+EMG21	emg	V	R1	forearm flexors	Grid1	E21
+EMG22	emg	V	R1	forearm flexors	Grid1	E22
+EMG23	emg	V	R1	forearm flexors	Grid1	E23
+EMG24	emg	V	R1	forearm flexors	Grid1	E24
+EMG25	emg	V	R1	forearm flexors	Grid1	E25
+EMG26	emg	V	R1	forearm flexors	Grid1	E26
+EMG27	emg	V	R1	forearm flexors	Grid1	E27
+EMG28	emg	V	R1	forearm flexors	Grid1	E28
+EMG29	emg	V	R1	forearm flexors	Grid1	E29
+EMG30	emg	V	R1	forearm flexors	Grid1	E30
+EMG31	emg	V	R1	forearm flexors	Grid1	E31
+EMG32	emg	V	R1	forearm flexors	Grid1	E32
+EMG33	emg	V	R1	forearm flexors	Grid1	E33
+EMG34	emg	V	R1	forearm flexors	Grid1	E34
+EMG35	emg	V	R1	forearm flexors	Grid1	E35
+EMG36	emg	V	R1	forearm flexors	Grid1	E36
+EMG37	emg	V	R1	forearm flexors	Grid1	E37
+EMG38	emg	V	R1	forearm flexors	Grid1	E38
+EMG39	emg	V	R1	forearm flexors	Grid1	E39
+EMG40	emg	V	R1	forearm flexors	Grid1	E40
+EMG41	emg	V	R1	forearm flexors	Grid1	E41
+EMG42	emg	V	R1	forearm flexors	Grid1	E42
+EMG43	emg	V	R1	forearm flexors	Grid1	E43
+EMG44	emg	V	R1	forearm flexors	Grid1	E44
+EMG45	emg	V	R1	forearm flexors	Grid1	E45
+EMG46	emg	V	R1	forearm flexors	Grid1	E46
+EMG47	emg	V	R1	forearm flexors	Grid1	E47
+EMG48	emg	V	R1	forearm flexors	Grid1	E48
+EMG49	emg	V	R1	forearm flexors	Grid1	E49
+EMG50	emg	V	R1	forearm flexors	Grid1	E50
+EMG51	emg	V	R1	forearm flexors	Grid1	E51
+EMG52	emg	V	R1	forearm flexors	Grid1	E52
+EMG53	emg	V	R1	forearm flexors	Grid1	E53
+EMG54	emg	V	R1	forearm flexors	Grid1	E54
+EMG55	emg	V	R1	forearm flexors	Grid1	E55
+EMG56	emg	V	R1	forearm flexors	Grid1	E56
+EMG57	emg	V	R1	forearm flexors	Grid1	E57
+EMG58	emg	V	R1	forearm flexors	Grid1	E58
+EMG59	emg	V	R1	forearm flexors	Grid1	E59
+EMG60	emg	V	R1	forearm flexors	Grid1	E60
+EMG61	emg	V	R1	forearm flexors	Grid1	E61
+EMG62	emg	V	R1	forearm flexors	Grid1	E62
+EMG63	emg	V	R1	forearm flexors	Grid1	E63
+EMG64	emg	V	R1	forearm flexors	Grid1	E64
+EMG65	emg	V	R2	forearm extensors	Grid2	E65
+EMG66	emg	V	R2	forearm extensors	Grid2	E66
+EMG67	emg	V	R2	forearm extensors	Grid2	E67
+EMG68	emg	V	R2	forearm extensors	Grid2	E68
+EMG69	emg	V	R2	forearm extensors	Grid2	E69
+EMG70	emg	V	R2	forearm extensors	Grid2	E70
+EMG71	emg	V	R2	forearm extensors	Grid2	E71
+EMG72	emg	V	R2	forearm extensors	Grid2	E72
+EMG73	emg	V	R2	forearm extensors	Grid2	E73
+EMG74	emg	V	R2	forearm extensors	Grid2	E74
+EMG75	emg	V	R2	forearm extensors	Grid2	E75
+EMG76	emg	V	R2	forearm extensors	Grid2	E76
+EMG77	emg	V	R2	forearm extensors	Grid2	E77
+EMG78	emg	V	R2	forearm extensors	Grid2	E78
+EMG79	emg	V	R2	forearm extensors	Grid2	E79
+EMG80	emg	V	R2	forearm extensors	Grid2	E80
+EMG81	emg	V	R2	forearm extensors	Grid2	E81
+EMG82	emg	V	R2	forearm extensors	Grid2	E82
+EMG83	emg	V	R2	forearm extensors	Grid2	E83
+EMG84	emg	V	R2	forearm extensors	Grid2	E84
+EMG85	emg	V	R2	forearm extensors	Grid2	E85
+EMG86	emg	V	R2	forearm extensors	Grid2	E86
+EMG87	emg	V	R2	forearm extensors	Grid2	E87
+EMG88	emg	V	R2	forearm extensors	Grid2	E88
+EMG89	emg	V	R2	forearm extensors	Grid2	E89
+EMG90	emg	V	R2	forearm extensors	Grid2	E90
+EMG91	emg	V	R2	forearm extensors	Grid2	E91
+EMG92	emg	V	R2	forearm extensors	Grid2	E92
+EMG93	emg	V	R2	forearm extensors	Grid2	E93
+EMG94	emg	V	R2	forearm extensors	Grid2	E94
+EMG95	emg	V	R2	forearm extensors	Grid2	E95
+EMG96	emg	V	R2	forearm extensors	Grid2	E96
+EMG97	emg	V	R2	forearm extensors	Grid2	E97
+EMG98	emg	V	R2	forearm extensors	Grid2	E98
+EMG99	emg	V	R2	forearm extensors	Grid2	E99
+EMG100	emg	V	R2	forearm extensors	Grid2	E100
+EMG101	emg	V	R2	forearm extensors	Grid2	E101
+EMG102	emg	V	R2	forearm extensors	Grid2	E102
+EMG103	emg	V	R2	forearm extensors	Grid2	E103
+EMG104	emg	V	R2	forearm extensors	Grid2	E104
+EMG105	emg	V	R2	forearm extensors	Grid2	E105
+EMG106	emg	V	R2	forearm extensors	Grid2	E106
+EMG107	emg	V	R2	forearm extensors	Grid2	E107
+EMG108	emg	V	R2	forearm extensors	Grid2	E108
+EMG109	emg	V	R2	forearm extensors	Grid2	E109
+EMG110	emg	V	R2	forearm extensors	Grid2	E110
+EMG111	emg	V	R2	forearm extensors	Grid2	E111
+EMG112	emg	V	R2	forearm extensors	Grid2	E112
+EMG113	emg	V	R2	forearm extensors	Grid2	E113
+EMG114	emg	V	R2	forearm extensors	Grid2	E114
+EMG115	emg	V	R2	forearm extensors	Grid2	E115
+EMG116	emg	V	R2	forearm extensors	Grid2	E116
+EMG117	emg	V	R2	forearm extensors	Grid2	E117
+EMG118	emg	V	R2	forearm extensors	Grid2	E118
+EMG119	emg	V	R2	forearm extensors	Grid2	E119
+EMG120	emg	V	R2	forearm extensors	Grid2	E120
+EMG121	emg	V	R2	forearm extensors	Grid2	E121
+EMG122	emg	V	R2	forearm extensors	Grid2	E122
+EMG123	emg	V	R2	forearm extensors	Grid2	E123
+EMG124	emg	V	R2	forearm extensors	Grid2	E124
+EMG125	emg	V	R2	forearm extensors	Grid2	E125
+EMG126	emg	V	R2	forearm extensors	Grid2	E126
+EMG127	emg	V	R2	forearm extensors	Grid2	E127
+EMG128	emg	V	R2	forearm extensors	Grid2	E128

emg_examples/sub-s5TwoHDsEMG/emg/sub-s5TwoHDsEMG_task-isometric_electrodes.json

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+{
+    "Coordsystem": {
+        "forearm-coordsystem":{ 
+            "EMGCoordinateUnits": "percent",
+            "EMGCoordinateSystemDescription": "X: RSP → USP; Y: Right-hand rule (limits: Olecranon Process → Cubital Fossa); Z: midpoint RSP-USP → LHE; Radial Styloid Process (RSP); Ulnar Styloid Process (USP), Lateral Humerus Epicondyle (LHE), Posterior Elbow (Olecranon Process)"
+        },
+        "grid1-coordsystem":{ 
+            "EMGCoordinateUnits": "mm",
+            "EMGCoordinateSystemDescription": "The location of the electgrodes with respect to electrode one (1) is given in millimeters. The x-axis is left to right, the y-axis is bottom to top. note: the z-axis is not used.",
+            "EMGCoordSysAnchor":{
+                "System": "forearm-coordsystem",
+                "AnchorElectrode": "E1",
+                "AnchorCoordinate": [10,80,80]
+            }
+        },
+        "grid2-coordsystem":{ 
+            "EMGCoordinateUnits": "mm",
+            "EMGCoordinateSystemDescription": "The location of the electgrodes with respect to electrode one (1) is given in millimeters. The x-axis is left to right, the y-axis is bottom to top. note: the z-axis is not used.",
+            "EMGCoordSysAnchor":{
+                "System": "forearm-coordsystem",
+                "AnchorElectrode": "E65",
+                "AnchorCoordinate": [10,0,80]
+            }
+        }
+    }
+}