Merge branch 'master' into emg_examples

Author: neuromechanist

.github/workflows/validate_datasets.yml

@@ -15,6 +15,10 @@ concurrency:
   group: ${{ github.ref }}
   cancel-in-progress: true
 
+defaults:
+  run:
+    shell: bash
+
 jobs:
   build:
     strategy:
@@ -47,23 +51,20 @@ jobs:
       if: matrix.bids-validator == 'stable'
       run: |
           deno install -Agf -n bids-validator jsr:@bids/validator
-      shell: bash
 
     - name: Install BIDS validator (main)
       if: matrix.bids-validator == 'main'
       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
-      shell: bash
 
     - 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
         deno compile -A -o $HOME/.deno/bin/bids-validator src/bids-validator.ts
-      shell: bash
 
     - name: Install BIDS validator (legacy)
       if: "matrix.bids-validator == 'legacy'"
@@ -78,7 +79,6 @@ jobs:
         echo "node\n----"; node --version
         echo "npm\n----"; npm --version
         echo "bids-validator"; bids-validator --version
-      shell: bash
 
     - name: Check that no large files are present
       if: "matrix.bids-validator == 'stable'"
@@ -93,17 +93,22 @@ jobs:
             echo "$found"
             exit 1;
         fi
-      shell: bash
 
     - name: Skip legacy validation for post-legacy datasets
-      run: for DS in mrs_* dwi_deriv; do touch $DS/.SKIP_VALIDATION; done
+      run: for DS in mrs_* dwi_deriv pheno004; do touch $DS/.SKIP_VALIDATION; done
       if: matrix.bids-validator == 'legacy'
-      shell: bash
 
-    - name: Skip stable validation for datasets with unreleased features
-      run: for DS in dwi_deriv; do touch $DS/.SKIP_VALIDATION; done
+    - name: Skip stable validation for datasets with unreleased validator features
+      # Replace ${EMPTY} with dataset patterns, when this is needed
+      # Reset to "for DS in ${EMPTY}; ..." after a validator release
+      run: for DS in ${EMPTY}; do touch $DS/.SKIP_VALIDATION; done
+      if: matrix.bids-validator == 'stable'
+
+    - 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
       if: matrix.bids-validator != 'dev'
-      shell: bash
 
     - name: Set BIDS_SCHEMA variable for dev version
       if: matrix.bids-validator == 'dev'
@@ -117,4 +122,3 @@ jobs:
       run: |
         cat ./run_tests.sh
         ./run_tests.sh
-      shell: bash

README.md

@@ -368,3 +368,14 @@ DO NOT EDIT DIRECTLY.
 | [qmri_sa2rage](https://github.com/bids-standard/bids-examples/tree/master/qmri_sa2rage)     | Fast B1+ mapping using SA2RAGE                                                           | fmap        | TB1SRGE                                                | `not publicly available`      | [@agahkarakuzu](https://github.com/agahkarakuzu)             |
 | [qmri_tb1tfl](https://github.com/bids-standard/bids-examples/tree/master/qmri_tb1tfl)       | B1+ mapping with TurboFLASH readout.                                                     | fmap        | TB1TFL                                                 | `not publicly available`      | [@agahkarakuzu](https://github.com/agahkarakuzu)             |
 | [qmri_vfa](https://github.com/bids-standard/bids-examples/tree/master/qmri_vfa)             | Variable Flip Angle T1 mapping. Includes an Actual Flip Angle (AFI) B1+ mapping example. | anat, fmap  | TB1AFI, VFA                                            | [link](https://osf.io/k4bs5/) | [@agahkarakuzu](https://github.com/agahkarakuzu)             |
+
+### Phenotype
+
+<!--
+TABLE BELOW IS GENERATED AUTOMATICALLY.
+DO NOT EDIT DIRECTLY.
+-->
+
+| name                                                                            | description                                                      | datatypes       | suffixes   | link to full data   | maintained by                            |
+|:--------------------------------------------------------------------------------|:-----------------------------------------------------------------|:----------------|:-----------|:--------------------|:-----------------------------------------|
+| [pheno004](https://github.com/bids-standard/bids-examples/tree/master/pheno004) | Minimal dataset with subjects with imaging and/or phenotype data | phenotype, anat | T1w        | n/a                 | [@ericearl](https://github.com/ericearl) |

dataset_listing.tsv

@@ -82,6 +82,7 @@ mrs_fmrs	Functional MRS data involving a pain stimulus task from 15 subjects	[li
 2d_mb_pcasl	Siemens 2D MultiBand Multi-delay PCASL (m0 and noRF included within timeseries)	[link](https://osf.io/xrkc4/)	[@aptinis](https://github.com/aptinis)	anat, fmap, perf	T1w, asl, aslcontext, epi
 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_CustomBipolar	Custom-made bipolar EMG recording setup with electrodes on flexors of the lower arm	emg	channels, emg	n/a	@neuromechanist
 emg_CustomBipolarFace	EMG recording from facial muscles with many-to-many mapping between sensors and muscles	emg	channels, electrodes, emg	n/a	@neuromechanist
 emg_IndependentMod	Commercial bipolar EMG modules recording multiple muscles with wireless sensors	emg	channels, emg	n/a	@neuromechanist

docs/index.md

@@ -1 +1 @@
-The website listing BIDS examples can now be found on the [main BIDS website](https://bids-website.readthedocs.io/en/latest/datasets/examples.html).
+The website listing BIDS examples can now be found on the [main BIDS website](https://bids.neuroimaging.io/datasets/examples.html).

eeg_ds003645s_hed_demo/dataset_description.json

@@ -1,7 +1,7 @@
 {
     "Name": "Face processing MEEG dataset with HED annotation",
     "BIDSVersion": "1.9.0",
-    "HEDVersion": "8.2.0",
+    "HEDVersion": "8.3.0",
     "License": "CC0",
     "Authors": [
         "Daniel G. Wakeman",

eeg_matchingpennies/dataset_description.json

@@ -14,5 +14,5 @@
     ],
     "DatasetDOI": "10.17605/OSF.IO/CJ2DR",
     "DatasetType": "raw",
-    "HEDVersion": "8.0.0"
+    "HEDVersion": ["8.3.0"]
 }

eeg_matchingpennies/task-matchingpennies_events.json

@@ -55,10 +55,10 @@
             "raised-right/match-true": "raised right hand, bci predicted right hand"
         },
         "HED": {
-            "raised-left/match-true": "(Agent-action, Participant-response, (Lift, (Hand, (Left-side-of, Experiment-participant))), (Release, (Mouse-button, (Left-side-of, Experiment-participant)))), (Delay, Duration, (Approximately-equal-to, Time-block/68 ms)), (Sensory-event, Visual-presentation, (Drawing, (ID/left_hand.png, Hand, (Left-side-of, Computer-screen))), (Feedback, Penalty)), Description/Subject raised left hand and computer presented image of hand to left side",
-            "raised-left/match-false": "(Agent-action, Participant-response, (Lift, (Hand, (Left-side-of, Experiment-participant))), (Release, (Mouse-button, (Left-side-of, Experiment-participant)))), (Delay, Duration, (Approximately-equal-to, Time-block/68 ms)), (Sensory-event, Visual-presentation, (Drawing, (ID/right_hand.png, Hand, (Right-side-of, Computer-screen))), (Feedback, Reward)), Description/Subject raised left hand and computer presented image of hand to right side",
-            "raised-right/match-true": "(Agent-action, Participant-response, (Lift, (Hand, (Right-side-of, Experiment-participant))), (Release, (Mouse-button, (Right-side-of, Experiment-participant)))), (Delay, Duration, (Approximately-equal-to, Time-block/68 ms)), (Sensory-event, Visual-presentation, (Drawing, (ID/right_hand.png, Hand, (Right-side-of, Computer-screen))), (Feedback, Penalty)), Description/Subject raised right hand and computer presented image of hand to right side",
-            "raised-right/match-false": "(Agent-action, Participant-response, (Lift, (Hand, (Right-side-of, Experiment-participant))), (Release, (Mouse-button, (Right-side-of, Experiment-participant)))), (Delay, Duration, (Approximately-equal-to, Time-block/68 ms)), (Sensory-event, Visual-presentation, (Drawing, (ID/left_hand.png, Hand, (Left-side-of, Computer-screen))), (Feedback, Reward)), Description/Subject raised right hand and computer presented image of hand to left side"
+            "raised-left/match-true": "(Agent-action, Participant-response, (Lift, (Hand, (Left-side-of, Experiment-participant))), (Release, (Mouse-button, (Left-side-of, Experiment-participant)))), (Sensory-event, Visual-presentation, (Drawing, (ID/left_hand.png, Hand, (Left-side-of, Computer-screen))), (Feedback, Penalty)), Description/Subject raised left hand and computer presented image of hand to left side. Time-block delayed for about 60 ms.",
+            "raised-left/match-false": "(Agent-action, Participant-response, (Lift, (Hand, (Left-side-of, Experiment-participant))), (Release, (Mouse-button, (Left-side-of, Experiment-participant)))),  (Sensory-event, Visual-presentation, (Drawing, (ID/right_hand.png, Hand, (Right-side-of, Computer-screen))), (Feedback, Reward)), Description/Subject raised left hand and computer presented image of hand to right side. ime-block delayed for about 60 ms.",
+            "raised-right/match-true": "(Agent-action, Participant-response, (Lift, (Hand, (Right-side-of, Experiment-participant))), (Release, (Mouse-button, (Right-side-of, Experiment-participant)))), (Sensory-event, Visual-presentation, (Drawing, (ID/right_hand.png, Hand, (Right-side-of, Computer-screen))), (Feedback, Penalty)), Description/Subject raised right hand and computer presented image of hand to right side. ime-block delayed for about 60 ms.",
+            "raised-right/match-false": "(Agent-action, Participant-response, (Lift, (Hand, (Right-side-of, Experiment-participant))), (Release, (Mouse-button, (Right-side-of, Experiment-participant)))),  (Sensory-event, Visual-presentation, (Drawing, (ID/left_hand.png, Hand, (Left-side-of, Computer-screen))), (Feedback, Reward)), Description/Subject raised right hand and computer presented image of hand to left side. ime-block delayed for about 60 ms."
         }
     },
     "stage": {

mkdocs.yml

@@ -2,7 +2,7 @@ site_name: bids-examples
 
 nav:
     - The BIDS examples:
-      - Examples: https://bids-website.readthedocs.io/en/latest/datasets/examples.html
+      - Examples: https://bids.neuroimaging.io/datasets/examples.html
       - Contributing: CONTRIBUTING.md
 
 theme:

pheno004/README.md

@@ -0,0 +1,23 @@
+# BEP036 example dataset 04: One imaging-only, one phenotypic-only, and one with both imaging and phenotypic data
+
+This dataset contains imaging data and phenotypic data from one subject, only imaging data for another subject, and only phenotypic data for a third subject. Phenotype and imaging data were collected at the same session. The file tree is as follows:
+
+```ascii
+📦pheno004
+ ┣ 📂phenotype
+ ┃ ┣ 📜ace.json
+ ┃ ┣ 📜ace.tsv
+ ┃ ┣ 📜demographics.json
+ ┃ ┗ 📜demographics.tsv
+ ┣ 📂sub-01
+ ┃ ┗ 📂anat
+ ┃ ┃ ┣ 📜sub-01_T1w.json
+ ┃ ┃ ┗ 📜sub-01_T1w.nii.gz
+ ┣ 📂sub-02
+ ┃ ┗ 📂anat
+ ┃ ┃ ┣ 📜sub-02_T1w.json
+ ┃ ┃ ┗ 📜sub-02_T1w.nii.gz
+ ┣ 📜participants.json
+ ┣ 📜participants.tsv
+ ┗ 📜README.md
+```

pheno004/dataset_description.json

@@ -0,0 +1,12 @@
+{
+    "Name": "Mixed Phenotype+Participants",
+    "BIDSVersion": "1.11.0",
+    "License": "CC0",
+    "Authors": [
+        "Eric Earl",
+        "Arshitha Basavaraj",
+        "Samuel Guay",
+        "Sebastian Urchs"
+    ],
+    "Acknowledgements": "Acknowledgements"
+}