[ENH] BEP042 - EMG examples

.codespellrc

@@ -1,4 +1,4 @@
 [codespell]
-skip = .git,env,venv,ds*,asl*,qmr*,genetics*,fnirs*,eeg*,meg*,pet*,ieeg*,motion*,synthetic*
+skip = .git,env,venv,ds*,asl*,qmr*,genetics*,fnirs*,eeg*,meg*,pet*,ieeg*,motion*,synthetic*,emg*
 builtin = clear,rare
-ignore-words-list = nd,te
+ignore-words-list = nd,te,FLE

.github/workflows/validate_datasets.yml

@@ -69,17 +69,19 @@ jobs:
       run: |
         # If unmerged validator PRs are needed for testing, you can use
         # https://github.com/<FORK>/bids-validator/raw/<BRANCH>/bids-validator/src/bids-validator.ts
-        deno install -Agf https://github.com/bids-standard/bids-validator/raw/deno-build/bids-validator.js
+         deno install -Agf https://github.com/bids-standard/bids-validator/raw/deno-build/bids-validator.js
 
     - name: Install BIDS validator (dev)
       if: matrix.bids-validator == 'dev'
       run: |
         git clone -b dev https://github.com/bids-standard/bids-validator/ ../bids-validator
         cd ../bids-validator
+        git fetch origin refs/pull/268/head
+        git checkout FETCH_HEAD
         deno compile -A -o $HOME/.deno/bin/bids-validator src/bids-validator.ts
 
     - name: Install BIDS validator (legacy)
-      if: "matrix.bids-validator == 'legacy'"
+      if: matrix.bids-validator == 'legacy'
       run: |
         npm install -g bids-validator
 
@@ -93,7 +95,7 @@ jobs:
         echo "bids-validator"; bids-validator --version
 
     - name: Check that no large files are present
-      if: "matrix.bids-validator == 'stable'"
+      if: matrix.bids-validator == 'stable'
       run: |
         echo "Checking for big files ..."
         found=`find . -not -path "./.git*" -type f -size +500k`
@@ -119,7 +121,7 @@ jobs:
     - name: Skip main validation for datasets with unreleased spec features
       # Replace ${EMPTY} with dataset patterns, when this is needed
       # Reset to "for DS in ${EMPTY}; ..." after a spec release
-      run: for DS in dwi_deriv pheno004; do touch $DS/.SKIP_VALIDATION; done
+      run: for DS in emg_*; do touch $DS/.SKIP_VALIDATION; done
       if: matrix.bids-validator != 'dev'
 
     - name: Set BIDS_SCHEMA variable for dev version
@@ -128,7 +130,7 @@ jobs:
       # Update this URL to the schema.json from PRs to the spec, when needed.
       # If this variable is unset, dev will generally track the latest development
       # release of https://jsr.io/@bids/schema
-      run: echo BIDS_SCHEMA=https://bids-specification.readthedocs.io/en/latest/schema.json >> $GITHUB_ENV
+      run: echo BIDS_SCHEMA=https://bids-specification--1998.org.readthedocs.build/en/1998/schema.json >> $GITHUB_ENV
 
     - name: Validate all BIDS datasets using bids-validator
       run: |

README.md

@@ -164,6 +164,23 @@ DO NOT EDIT DIRECTLY.
 | [eeg_matchingpennies](https://github.com/bids-standard/bids-examples/tree/master/eeg_matchingpennies)             | Offline data of BCI experiment decoding left vs. right hand movement. BrainVision data format (.eeg, .vhdr, .vmrk) | eeg         | channels, eeg, events                          | [link](https://doi.org/10.17605/OSF.IO/CJ2DR)   | [@sappelhoff](https://github.com/sappelhoff)   |
 | [eeg_rishikesh](https://github.com/bids-standard/bids-examples/tree/master/eeg_rishikesh)                         | Mind wandering experiment. EEG data in Biosemi (.bdf) format                                                       | eeg         | channels, eeg, events                          | [link](https://openneuro.org/datasets/ds001787) | [@arnodelorme](https://github.com/arnodelorme) |
 
+### EMG
+
+<!--
+TABLE BELOW IS GENERATED AUTOMATICALLY.
+DO NOT EDIT DIRECTLY.
+-->
+
+| name                                                                                                          | description                                                                                           | datatypes   | suffixes                                                          | link to full data | maintained by                        |
+|:--------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------|:------------|:------------------------------------------------------------------|:------------------|:-------------------------------------|
+| [emg_ConcurrentIndependentUnits](https://github.com/bids-standard/bids-examples/tree/master/emg_ConcurrentIndependentUnits) | Concurrent EMG recording with multiple independent recording units at different sampling rates | emg         | channels, electrodes, coordsystem, emg, events             | n/a               | [@neuromechanist](https://github.com/neuromechanist) |
+| [emg_CustomBipolar](https://github.com/bids-standard/bids-examples/tree/master/emg_CustomBipolar)             | Custom-made bipolar EMG recording setup with electrodes on flexors of the lower arm                   | emg         | channels, emg                                                     | n/a               | [@neuromechanist](https://github.com/neuromechanist) |
+| [emg_CustomBipolarFace](https://github.com/bids-standard/bids-examples/tree/master/emg_CustomBipolarFace)     | EMG recording from facial muscles with many-to-many mapping between sensors and muscles               | emg         | channels, coordsystem, electrodes, emg, events                    | n/a               | [@neuromechanist](https://github.com/neuromechanist) |
+| [emg_IndependentMod](https://github.com/bids-standard/bids-examples/tree/master/emg_IndependentMod)           | Commercial bipolar EMG modules recording multiple muscles with wireless sensors                       | emg         | channels, emg                                                     | n/a               | [@neuromechanist](https://github.com/neuromechanist) |
+| [emg_MultiBodyParts](https://github.com/bids-standard/bids-examples/tree/master/emg_MultiBodyParts)           | EMG recording from multiple body parts with different electrode types                                 | emg         | channels, electrodes, coordsystem, emg                            | n/a               | [@neuromechanist](https://github.com/neuromechanist) |
+| [emg_TwoHDsEMG](https://github.com/bids-standard/bids-examples/tree/master/emg_TwoHDsEMG)                     | High-density EMG grid recordings from two body parts demonstrating grid placement documentation       | emg         | channels, electrodes, coordsystem, emg                            | n/a               | [@neuromechanist](https://github.com/neuromechanist) |
+| [emg_TwoWristbands](https://github.com/bids-standard/bids-examples/tree/master/emg_TwoWristbands)             | EMG recordings using two wristbands with dry electrodes to capture forearm muscle activity            | emg         | channels, electrodes, coordsystem, emg                            | n/a               | [@neuromechanist](https://github.com/neuromechanist) |
+
 ### DWI
 
 <!--
@@ -220,7 +237,7 @@ DO NOT EDIT DIRECTLY.
 | name                                                                            | description                                                                                                          | datatypes                       | suffixes                                                                                                       | link to full data                                              | maintained by                              |
 |:--------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------|:--------------------------------|:---------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------|:-------------------------------------------|
 | [ds000117](https://github.com/bids-standard/bids-examples/tree/master/ds000117) | A multi-subject, multi-modal human neuroimaging dataset of 19 subjects on a MEG visual task                          | anat, beh, dwi, fmap, func, meg | FLASH, T1w, bold, channels, coordsystem, dwi, events, headshape, magnitude1, magnitude2, meg, phasediff, scans | [link](https://openneuro.org/datasets/ds000117/)               | [@RikHenson](https://github.com/RikHenson) |
-| [ds000246](https://github.com/bids-standard/bids-examples/tree/master/ds000246) | Auditory dataset used for Brainstorm’s general online tutorial                                                       | anat, meg                       | T1w, channels, coordsystem, headshape, meg, photo, scans                                                       | [link](https://openneuro.org/datasets/ds000246/versions/00001) | [@guiomar](https://github.com/guiomar)     |
+| [ds000246](https://github.com/bids-standard/bids-examples/tree/master/ds000246) | Auditory dataset used for Brainstorm's general online tutorial                                                       | anat, meg                       | T1w, channels, coordsystem, headshape, meg, photo, scans                                                       | [link](https://openneuro.org/datasets/ds000246/versions/00001) | [@guiomar](https://github.com/guiomar)     |
 | [ds000247](https://github.com/bids-standard/bids-examples/tree/master/ds000247) | Five minutes, eyes-open, resting-state MEG data from 5 subjects. This is a sample from The Open MEG Archive (OMEGA). | anat, meg                       | T1w, channels, coordsystem, headshape, meg, scans                                                              | [link](https://openneuro.org/datasets/ds000247/versions/00001) | [@guiomar](https://github.com/guiomar)     |
 | [ds000248](https://github.com/bids-standard/bids-examples/tree/master/ds000248) | MNE sample data: Data with visual and auditory stimuli                                                               | anat, meg                       | FLASH, T1w, channels, coordsystem, events, meg, scans                                                          | [link](https://openneuro.org/datasets/ds000248/versions/00001) | [@agramfort](https://github.com/agramfort) |
 

dataset_listing.tsv

@@ -85,4 +85,11 @@ mrs_fmrs	Functional MRS data involving a pain stimulus task from 15 subjects	[li
 xeeg_hed_score	EEG and iEEG data with annotations of artifacts, seizures and modulators using HED-SCORE 		[@dorahermes](https://github.com/dorahermes)	anat, eeg, ieeg	T1w, channels, coordsystem, eeg, electrodes, events, ieeg
 dwi_deriv	exemplifies the storage of diffusion MRI derivates that may be generated on the Siemens XA platform.			dwi	dwi
 pheno004	Minimal dataset with subjects with imaging and/or phenotype data		[@ericearl](https://github.com/ericearl)	phenotype, anat	T1w
+emg_ConcurrentIndependentUnits	Concurrent EMG recording with multiple independent recording units at different sampling rates	n/a	[@neuromechanist](https://github.com/neuromechanist)	emg	channels, electrodes, coordsystem, emg, events
+emg_CustomBipolar	Custom-made bipolar EMG recording setup with electrodes on flexors of the lower arm	n/a	[@neuromechanist](https://github.com/neuromechanist)	emg	channels, emg
+emg_CustomBipolarFace	EMG recording from facial muscles with many-to-many mapping between sensors and muscles	n/a	[@neuromechanist](https://github.com/neuromechanist)	emg	channels, electrodes, coordsystem, emg
+emg_IndependentMod	Commercial bipolar EMG modules recording multiple muscles with wireless sensors	n/a	[@neuromechanist](https://github.com/neuromechanist)	emg	channels, electrodes, coordsystem, emg
+emg_MultiBodyParts	EMG recording from multiple body parts with different electrode types	n/a	[@neuromechanist](https://github.com/neuromechanist)	emg	channels, electrodes, coordsystem, emg
+emg_TwoHDsEMG	High-density EMG grid recordings from two body parts demonstrating grid placement documentation	n/a	[@neuromechanist](https://github.com/neuromechanist)	emg	channels, electrodes, coordsystem, emg
+emg_TwoWristbands	EMG recordings using two wristbands with dry electrodes to capture forearm muscle activity	n/a	[@neuromechanist](https://github.com/neuromechanist)	emg	channels, electrodes, coordsystem, emg
 mri_chunk	Example MRI dataset to illustrate BIDS chunk entity. A single subject, two chunks.		[@valosekj](https://github.com/valosekj)	anat	T1w

emg_CustomBipolar/README.md

@@ -0,0 +1,30 @@
+# EMG Custom Bipolar Example
+
+This dataset demonstrates documentation of a custom-made bipolar EMG system recording:
+- Single channel bipolar montage
+- Precise electrode placement using anatomical landmarks
+- Inter-electrode distance specifications
+
+## Dataset Structure
+
+The dataset includes a single subject with a custom bipolar EMG setup:
+
+```
+emg_CustomBipolar/
+├── dataset_description.json
+├── participants.json
+├── participants.tsv
+├── README.md
+└── sub-01/
+    └── emg/
+        ├── sub-01_task-holdWeight_channels.tsv
+        ├── sub-01_task-holdWeight_emg.edf
+        └── sub-01_task-holdWeight_emg.json
+```
+
+## Recording Details
+
+- **Electrode Setup**: Custom bipolar EMG recording from flexors of the lower arm
+- **Task**: Holding a weight to activate forearm flexors
+- **Electrode Placement**: Precise positioning using anatomical landmarks
+- **Inter-electrode Distance**: 2 cm between recording electrodes 

emg_CustomBipolar/dataset_description.json

@@ -0,0 +1,17 @@
+{
+  "Name": "EMG Custom Bipolar Example",
+  "License": "BSD 3-Clause",
+  "Authors": ["BEP042", "Contributors"],
+  "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",
+  "SourceDatasets": [{"URL": "n/a"}],
+  "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_CustomBipolar/participants.json

@@ -0,0 +1,21 @@
+{
+    "age": {
+        "Description": "Age in years",
+        "Units": "years"
+    },
+    "sex": {
+        "Description": "self-reported sex, one of M, F, or O",
+        "Levels": {
+            "M": "male",
+            "F": "female",
+            "O": "other"
+        }
+    },
+    "group": {
+        "Description": "Experimental group the participant belonged to",
+        "Levels": {
+            "control": "Control group",
+            "experiment": "Experimental group"
+        }
+    }
+} 

emg_CustomBipolar/participants.tsv

@@ -0,0 +1,2 @@
+participant_id	age	sex	group
+sub-01	24	F	control

emg_CustomBipolar/sub-01/emg/sub-01_task-holdWeight_channels.tsv

@@ -0,0 +1,2 @@
+name	type	units	target_muscle
+EMG1	EMG	V	Flexor carpi radialis, Pronator teres, Brachioradialis

emg_CustomBipolar/sub-01/emg/sub-01_task-holdWeight_emg.json

@@ -0,0 +1,16 @@
+{
+	"EMGChannelCount":1,
+	"EMGPlacementScheme":"Other",
+	"EMGPlacementSchemeDescription":"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",
+	"Manufacturer":"Custom",
+	"ManufacturersModelName":"Raspberry Pi",
+	"RecordingDuration":1.00,
+	"RecordingType":"continuous",
+	"SamplingFrequency":2000,
+	"TaskDescription":"The subject was holding an object with different weights for 5 seconds.",
+	"TaskName":"holdWeight",
+	"PowerLineFrequency":60,
+	"SoftwareFilters":"n/a"
+}

emg_CustomBipolarFace/README.md

@@ -0,0 +1,32 @@
+# EMG Custom Bipolar Face Example
+
+This dataset illustrates recording from facial muscles with:
+- One-to-many mapping between sensors and muscles
+- Functional localization for electrode placement
+- Recording from muscles without bony landmarks
+
+## Dataset Structure
+
+The dataset includes a single subject with custom bipolar EMG setup for facial muscles:
+
+```shell
+emg_CustomBipolarFace/
+├── dataset_description.json
+├── participants.json
+├── participants.tsv
+├── README.md
+└── sub-01/
+    └── emg/
+        ├── sub-01_task-talking_channels.tsv
+        ├── sub-01_task-talking_electrodes.json
+        ├── sub-01_task-talking_electrodes.tsv
+        ├── sub-01_task-talking_emg.edf
+        └── sub-01_task-talking_emg.json
+```
+
+## Recording Details
+
+- **Electrode Setup**: Custom bipolar EMG recordings from facial muscles
+- **Task**: Talking task with facial expressions
+- **Challenges**: Documentation of electrode placement on non-bony landmarks
+- **Muscles Recorded**: Multiple facial muscles (zygomaticus, frontalis, orbicularis oris)

emg_CustomBipolarFace/dataset_description.json

@@ -0,0 +1,17 @@
+{
+  "Name": "EMG Custom Bipolar Face Example",
+  "License": "BSD 3-Clause",
+  "Authors": ["BEP042", "Contributors"],
+  "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",
+  "SourceDatasets": [{"URL": "n/a"}],
+  "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_CustomBipolarFace/participants.json

@@ -0,0 +1,21 @@
+{
+    "age": {
+        "Description": "Age in years",
+        "Units": "years"
+    },
+    "sex": {
+        "Description": "self-reported sex, one of M, F, or O",
+        "Levels": {
+            "M": "male",
+            "F": "female",
+            "O": "other"
+        }
+    },
+    "group": {
+        "Description": "Experimental group the participant belonged to",
+        "Levels": {
+            "control": "Control group",
+            "experiment": "Experimental group"
+        }
+    }
+} 

emg_CustomBipolarFace/participants.tsv

@@ -0,0 +1,2 @@
+participant_id	age	sex	group
+sub-01	27	F	control

emg_CustomBipolarFace/sub-01/emg/sub-01_coordsystem.json

@@ -0,0 +1,5 @@
+{
+    "EMGCoordinateSystem": "Other",
+    "EMGCoordinateUnits": "percent",
+    "EMGCoordinateSystemDescription": "x: left helix-tragus junction (LHJ) → right helix-tragus junction (RHJ); y: inion → nasion; z: midpoint between mastoid processes → vertex"
+}

emg_CustomBipolarFace/sub-01/emg/sub-01_electrodes.tsv

@@ -0,0 +1,13 @@
+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_CustomBipolarFace/sub-01/emg/sub-01_task-talking_channels.tsv

@@ -0,0 +1,7 @@
+name	type	units	signal_electrode	reference	target_muscle
+EMG1	EMG	V	E1	E2	tongue, anterior belly of the digastric
+EMG2	EMG	V	E3	E4	levator angulis oris, zygomaticus major
+EMG3	EMG	V	E5	E6	levator angulis oris, zygomaticus major
+EMG4	EMG	V	E7	E8	platysma
+EMG5	EMG	V	E9	E10	orbicularis oris
+EMG6	EMG	V	E11	E12	tongue

emg_CustomBipolarFace/sub-01/emg/sub-01_task-talking_emg.json

@@ -0,0 +1,16 @@
+{
+	"EMGChannelCount":6,
+	"EMGPlacementScheme":"Other",
+	"EMGPlacementSchemeDescription":"Electrodes placed over articulatory muscles on the lower face.",
+	"EMGReference":"Behind the ear (Mastoid)",
+	"EMGGround":"n/a",
+	"Manufacturer":"Custom",
+	"ManufacturersModelName":"n/a",
+	"RecordingDuration":1.00,
+	"RecordingType":"continuous",
+	"SamplingFrequency":2000,
+	"TaskDescription":"Subject performed speech tasks.",
+	"TaskName":"talking",
+	"PowerLineFrequency":60,
+	"SoftwareFilters":"n/a"
+}

emg_CustomBipolarFace/sub-01/emg/sub-01_task-talking_events.json

@@ -0,0 +1,13 @@
+{
+    "trial_type": {
+        "LongName": "Event category",
+        "Description": "Type of stimulus",
+        "Levels": {
+            "foo": "Foo stimulus was present",
+            "bar": "Bar stimulus was present"
+        }
+    },
+    "StimulusPresentation": {
+        "Code": "https://github.com/LABSN/expyfun/tree/58634c159404ea64e1d89c0b4e70bd13c2b77723"
+    }
+}

emg_CustomBipolarFace/sub-01/emg/sub-01_task-talking_events.tsv

@@ -0,0 +1,2 @@
+onset	duration	trial_type
+0.0	0	foo