Merge remote-tracking branch 'upstream/master' into bep038

effigies · effigies · commit d7d52a7b57b8 · 2025-11-04T12:09:19.000-05:00
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -6,3 +6,7 @@ updates:
     directory: "/"
     schedule:
       interval: "weekly"
+    groups:
+      actions-infrastructure:
+        patterns:
+         - "actions/*"
diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
@@ -17,7 +17,7 @@ jobs:
         steps:
             -   name: Checkout 🛎️
                 uses: actions/checkout@v5
-            -   uses: actions/setup-python@v5
+            -   uses: actions/setup-python@v6
                 with:
                     python-version: "3.11"
             -   name: Install and Build 🔧
diff --git a/.github/workflows/validate_datasets.yml b/.github/workflows/validate_datasets.yml
@@ -8,6 +8,7 @@ on:
     branches: [master, main, 'bep*']
   schedule:
     - cron: "0 4 * * 1"
+  workflow_dispatch:
 
 concurrency:
   group: ${{ github.ref }}
@@ -36,7 +37,7 @@ jobs:
 
     - name: Set up Node.js
       if: matrix.bids-validator == 'legacy'
-      uses: actions/setup-node@v4
+      uses: actions/setup-node@v6
       with:
         node-version: 22
 
diff --git a/README.md b/README.md
@@ -324,13 +324,14 @@ TABLE BELOW IS GENERATED AUTOMATICALLY.
 DO NOT EDIT DIRECTLY.
 -->
 
-| name                                                                        | description     | datatypes   | suffixes         | link to full data                                | maintained by                                |
-|:----------------------------------------------------------------------------|:----------------|:------------|:-----------------|:-------------------------------------------------|:---------------------------------------------|
-| [pet001](https://github.com/bids-standard/bids-examples/tree/master/pet001) | T1w, PET, blood | anat, pet   | T1w, blood, pet  | n/a                                              | [@mnoergaard](https://github.com/mnoergaard) |
-| [pet002](https://github.com/bids-standard/bids-examples/tree/master/pet002) | T1w, PET        | anat, pet   | T1w, pet         | [link](https://openneuro.org/datasets/ds001420/) | [@mnoergaard](https://github.com/mnoergaard) |
-| [pet003](https://github.com/bids-standard/bids-examples/tree/master/pet003) | T1w, PET, blood | anat, pet   | T1w, blood, pet  | n/a                                              | [@mnoergaard](https://github.com/mnoergaard) |
-| [pet004](https://github.com/bids-standard/bids-examples/tree/master/pet004) | PET, blood      | pet         | blood, pet       | n/a                                              | [@mnoergaard](https://github.com/mnoergaard) |
-| [pet005](https://github.com/bids-standard/bids-examples/tree/master/pet005) | T1w, PET        | anat, pet   | T1w, events, pet | n/a                                              | [@mnoergaard](https://github.com/mnoergaard) |
+| name                                                                        | description     | datatypes   | suffixes         | link to full data                                | maintained by                                    |
+|:----------------------------------------------------------------------------|:----------------|:------------|:-----------------|:-------------------------------------------------|:-------------------------------------------------|
+| [pet001](https://github.com/bids-standard/bids-examples/tree/master/pet001) | T1w, PET, blood | anat, pet   | T1w, blood, pet  | n/a                                              | [@mnoergaard](https://github.com/mnoergaard)     |
+| [pet002](https://github.com/bids-standard/bids-examples/tree/master/pet002) | T1w, PET        | anat, pet   | T1w, pet         | [link](https://openneuro.org/datasets/ds001420/) | [@mnoergaard](https://github.com/mnoergaard)     |
+| [pet003](https://github.com/bids-standard/bids-examples/tree/master/pet003) | T1w, PET, blood | anat, pet   | T1w, blood, pet  | n/a                                              | [@mnoergaard](https://github.com/mnoergaard)     |
+| [pet004](https://github.com/bids-standard/bids-examples/tree/master/pet004) | PET, blood      | pet         | blood, pet       | n/a                                              | [@mnoergaard](https://github.com/mnoergaard)     |
+| [pet005](https://github.com/bids-standard/bids-examples/tree/master/pet005) | T1w, PET        | anat, pet   | T1w, events, pet | n/a                                              | [@mnoergaard](https://github.com/mnoergaard)     |
+| [pet006](https://github.com/bids-standard/bids-examples/tree/master/pet006) | PET             | pet         | pet              | n/a                                              | [@bendhouseart](https://github.com/bendhouseart) |
 
 ### qMRI
 
diff --git a/dataset_listing.tsv b/dataset_listing.tsv
@@ -57,6 +57,7 @@ pet002	T1w, PET	[link](https://openneuro.org/datasets/ds001420/)	[@mnoergaard](h
 pet003	T1w, PET, blood		[@mnoergaard](https://github.com/mnoergaard)	anat, pet	T1w, blood, pet
 pet004	PET, blood		[@mnoergaard](https://github.com/mnoergaard)	pet	blood, pet
 pet005	T1w, PET		[@mnoergaard](https://github.com/mnoergaard)	anat, pet	T1w, events, pet
+pet006	PET		[@bendhouseart](https://github.com/bendhouseart)	pet	pet
 micr_SEM	Example SEM dataset in PNG format with 1 sample imaged over 2 sessions	[link](https://doi.org/10.5281/zenodo.5498378)	[@jcohenadad](https://github.com/jcohenadad)	micr	SEM, photo, samples, sessions
 micr_SEMzarr	Example SEM dataset in PNG and OME-ZARR format with 1 sample imaged over 2 sessions		[@TheChymera](https://github.com/TheChymera)	micr	SEM, SPIM, samples, sessions
 micr_SPIM	Example SPIM dataset in OME-TIFF format with 2 samples from the same subject with 4 chunks each	[link](https://doi.org/10.5281/zenodo.5517223)	[@jcohenadad](https://github.com/jcohenadad)	micr	SPIM, photo, samples
diff --git a/eeg_ds003645s_hed_demo/sub-004/ses-1/eeg/sub-004_ses-1_task-FacePerception_run-1_events.tsv b/eeg_ds003645s_hed_demo/sub-004/ses-1/eeg/sub-004_ses-1_task-FacePerception_run-1_events.tsv
@@ -1,5 +1,5 @@
 onset	duration	event_type	face_type	rep_status	rep_lag	trial	value	stim_file
-24.26672727	n/a	show_face_initial	scrambled_face	first_show	n/a	1	4	s107.bmp
+24.26672727	n/a	show_face_initial	scrambled_face	first_show	n/a	1	17	s107.bmp
 25.11309091	n/a	show_circle	n/a	n/a	n/a	1	0	circle.bmp
 25.28036364	n/a	right_press	n/a	n/a	n/a	1	4096	n/a
 26.81309091	n/a	show_cross	n/a	n/a	n/a	2	1	cross.bmp
diff --git a/eeg_ds003645s_hed_demo/task-FacePerception_events.json b/eeg_ds003645s_hed_demo/task-FacePerception_events.json
@@ -95,22 +95,22 @@
   "value": {
     "Description": "Numerical event marker",
     "Levels": {
-      "x0": "Disappearance of face image and display of the inter-stimulus circle simultaneously",
-      "x1": "Disappearance of face image and display of the inter-stimulus circle simultaneously",
-      "x2": "Initial setup with left finger key press indicating above average symmetry",
-      "x3": "Initial setup with right finger key press indicating above average symmetry",
-      "x5": "Initial presentation of famous face",
-      "x6": "Immediate repeated  presentation of famous face",
-      "x7": "Delayed repeated  presentation of famous face",
-      "x13": "Initial presentation of unfamiliar face",
-      "x14": "Immediate repeated  presentation of unfamiliar face",
-      "x15": "Delayed repeated  presentation of unfamiliar face",
-      "x17": "Initial presentation of scrambled face",
-      "x18": "Immediate repeated  presentation of scrambled face",
-      "x19": "Delayed repeated  presentation of scrambled face",
-      "x256": "Left finger key press",
-      "x4096": "Right finger key press",
-	  "x4352": "Left and right finger key presses"
+      "0": "Disappearance of face image and display of the inter-stimulus circle simultaneously",
+      "1": "Disappearance of face image and display of the inter-stimulus circle simultaneously",
+      "2": "Initial setup with left finger key press indicating above average symmetry",
+      "3": "Initial setup with right finger key press indicating above average symmetry",
+      "5": "Initial presentation of famous face",
+      "6": "Immediate repeated  presentation of famous face",
+      "7": "Delayed repeated  presentation of famous face",
+      "13": "Initial presentation of unfamiliar face",
+      "14": "Immediate repeated  presentation of unfamiliar face",
+      "15": "Delayed repeated  presentation of unfamiliar face",
+      "17": "Initial presentation of scrambled face",
+      "18": "Immediate repeated  presentation of scrambled face",
+      "19": "Delayed repeated  presentation of scrambled face",
+      "256": "Left finger key press",
+      "4096": "Right finger key press",
+      "4352": "Left and right finger key presses"
     }
   }
 }
diff --git a/eeg_ds003645s_hed_library/task-FacePerception_events.json b/eeg_ds003645s_hed_library/task-FacePerception_events.json
@@ -107,31 +107,30 @@
     }
   },
   "hed_def_setup": {
-     "Description": "Metadata dictionary for gathering setup definitions",
-     "HED": {
-        "setup_def": "(Definition/Initialize-recording, (Recording))"
-      }
-
+    "Description": "Metadata dictionary for gathering setup definitions",
+    "HED": {
+      "setup_def": "(Definition/Initialize-recording, (Recording))"
+    }
   },
   "value": {
     "Description": "Numerical event marker",
     "Levels": {
-      "x0": "Disappearance of face image and display of the inter-stimulus circle simultaneously",
-      "x1": "Disappearance of face image and display of the inter-stimulus circle simultaneously",
-      "x2": "Initial setup with left finger key press indicating above average symmetry",
-      "x3": "Initial setup with right finger key press indicating above average symmetry",
-      "x5": "Initial presentation of famous face",
-      "x6": "Immediate repeated  presentation of famous face",
-      "x7": "Delayed repeated  presentation of famous face",
-      "x13": "Initial presentation of unfamiliar face",
-      "x14": "Immediate repeated  presentation of unfamiliar face",
-      "x15": "Delayed repeated  presentation of unfamiliar face",
-      "x17": "Initial presentation of scrambled face",
-      "x18": "Immediate repeated  presentation of scrambled face",
-      "x19": "Delayed repeated  presentation of scrambled face",
-      "x256": "Left finger key press",
-      "x4096": "Right finger key press",
-	  "x4352": "Left and right finger key presses"
+      "0": "Disappearance of face image and display of the inter-stimulus circle simultaneously",
+      "1": "Disappearance of face image and display of the inter-stimulus circle simultaneously",
+      "2": "Initial setup with left finger key press indicating above average symmetry",
+      "3": "Initial setup with right finger key press indicating above average symmetry",
+      "5": "Initial presentation of famous face",
+      "6": "Immediate repeated  presentation of famous face",
+      "7": "Delayed repeated  presentation of famous face",
+      "13": "Initial presentation of unfamiliar face",
+      "14": "Immediate repeated  presentation of unfamiliar face",
+      "15": "Delayed repeated  presentation of unfamiliar face",
+      "17": "Initial presentation of scrambled face",
+      "18": "Immediate repeated  presentation of scrambled face",
+      "19": "Delayed repeated  presentation of scrambled face",
+      "256": "Left finger key press",
+      "4096": "Right finger key press",
+      "4352": "Left and right finger key presses"
     }
   }
 }
diff --git a/eeg_rishikesh/task-meditation_events.json b/eeg_rishikesh/task-meditation_events.json
@@ -11,7 +11,8 @@
     "Description": "Type of event (different from EEGLAB convention)",
     "Levels": {
       "stimulus": "Onset of first question",
-      "response": "Response to question 1, 2 or 3"
+      "response": "Response to question 1, 2 or 3",
+      "STATUS": "Status event"
     }
   },
   "response_time": {
@@ -27,7 +28,8 @@
       "4": "Response 2 (this may be a response to question 1, 2 or 3)",
       "8": "Response 3 (this may be a response to question 1, 2 or 3)",
       "16": "Indicate involuntary response",
-      "128": "First question onset (most important marker)"
+      "128": "First question onset (most important marker)",
+      "254": "Status event"
     }
   }
 }
diff --git a/fnirs_automaticity/events.json b/fnirs_automaticity/events.json
@@ -31,11 +31,7 @@
   },
   "shown_stimulus": {
     "Description": "visual stimulus shown on the presentation screen",
-    "Levels": {
-      "white X": "small white fixation cross on the middle of the screen, indicating that the participant should relax and focus on the cross. At the beginning of a trial, a metronome sound of 1.5 Hz was played during the first 8 seconds of the white fixation cross.",
-      "red X": "small red fixation cross in the middle of the screen, indicating that the participant should start tapping/stepping the sequence (once) during the single-task conditions",
-      "QGCQOGCG": "random sequence of 8 letters (C, G, Q, or O) shown at random intervals (0.5-1.5 s) on the middle of the screen during the dual-task conditions. Participants needed to tap/step the sequence once, while simultaneously counting the letter G."
-    }
+    "Format": "string"
   },
   "reported_gs": {
     "Description": "Reported number of G's, as counted by the particpant during the dual-task conditions."
@@ -57,4 +53,4 @@
       "erroneous trial": "trial with more than 1 error in the performed sequence"
     }
   }
-}
+}
diff --git a/fnirs_automaticity/participants.tsv b/fnirs_automaticity/participants.tsv
@@ -1,6 +1,6 @@
 participant_id	sex	age	haircolor	skincolor	handedness	footedness	musicality	comfortlevel_begin	comfortlevel_end	included	reasonforexclusion	comfortlevel_before	comfortlevel_after	headcircumference	distance_NzIz	distance_LPARPA	reason_for_exclusion
 sub-06	M	29	blond	light	10	10	31	5.5	2.5	1	n/a	5.5	2.5	59	41	39.5	n/a
-sub-10	F	22	dark brown	light intermidiate	10	13	27	n/a	n/a	0	n/a	5	2	57	39	37	more than half of the channels with SCI < 0.7
+sub-10	F	22	dark brown	light intermediate	10	13	27	n/a	n/a	0	n/a	5	2	57	39	37	more than half of the channels with SCI < 0.7
 sub-19	F	22	light brown	very light	10	6	41	n/a	n/a	1	n/a	7.5	3	56	36	38	n/a
 sub-21	F	21	dark brown	light	10	10	9	n/a	n/a	1	n/a	7	4	55	37	35	n/a
 sub-27	F	25	light brown	light	10	3	7	n/a	n/a	1	n/a	7	2	54	37.5	36	n/a
@@ -11,7 +11,7 @@ sub-38	M	24	light brown	light	10	16	31	n/a	n/a	1	n/a	NA	NA	61	40	41	n/a
 sub-43	F	21	light brown	light	10	15	18	n/a	n/a	1	n/a	7	NA	58	39	38	n/a
 sub-44	M	24	blond	light	9	15	10	n/a	n/a	1	n/a	7.5	6.5	59	40	39	n/a
 sub-52	F	26	dark brown	light	10	16	33	n/a	n/a	1	n/a	7	4	57	39	35	n/a
-sub-53	M	27	completely black	light intermidiate	10	6	10	n/a	n/a	1	n/a	8	2	61	40	39	n/a
+sub-53	M	27	black	light intermediate	10	6	10	n/a	n/a	1	n/a	8	2	61	40	39	n/a
 sub-63	M	23	blond	light	10	13	32	n/a	n/a	1	n/a	4	3	57	39	39.5	n/a
 sub-67	F	22	light brown	light	10	5	32	n/a	n/a	1	n/a	8	NA	60	40	37	n/a
 sub-69	F	26	blond	light	9	12	26	n/a	n/a	1	n/a	7.5	4	58	40	39	n/a
diff --git a/genetics_ukbb/participants.json b/genetics_ukbb/participants.json
@@ -1,69 +1,73 @@
-{
-    "age": {
-        "LongName": "age",
-        "Description": "age of the participant",
-        "Units": "month"
-    },
-    "sex": {
-        "LongName": "sex",
-        "Description": "sex of the participant",
-        "Levels": {
-            "M": "male",
-            "F": "female"
-        }
-    },
-    "group": {
-        "LongName": "group",
-        "Description": "classification of participant based on study desease status",
-        "Levels": {
-            "patient": "patient",
-            "control": "control"
-        }
-    },
-    "genetic_id": {
-        "LongName": "genetic_id",
-        "Description": "Uniq sample ID per genotyped sample in genetic database"
-      },
-    "IDH": {
-        "LongName": "isocitrate dehydrogenase gene",
-        "Description": "mutation present or abscent",
-        "Levels": {
-            "yes": "present",
-            "no": "abscent"
-        }      },
-    "BatchID": {
-        "LongName": "BatchID",
-        "Description": "SNP array genotyping uniq batch ID per group of subjects",
-        "Levels": {
-            "b001": "Batch sequence number 1",
-            "b002": "Batch sequence number 2"
-        }
-      },
-      "VariationSetType": {
-            "LongName": "VariationSetType",
-            "Description": "Availability of SNV and/or CNV information",
-            "Levels": {
-                "SNV": "Single-nucleotide variants",
-                "CNV": "Copy-Number Variants",
-                "SNV/CNV": "Single-nucleotide variants/Copy-Number Variants"
-            }
-        },
-      "Assembly": {
-              "LongName": "Assembly",
-              "Description": "Reference genome from which the sample variations were computed",
-              "Levels": {
-                  "hg19": "Human genome version 19 equivalent to GRCh37 (Genome Reference consorcium of human build 37)",
-                  "hg38": "Human genome version 38 equivalent to GRCh38 (Genome Reference consorcium of human build 38)",
-                  "hg19/hg38": "Genome used to compute respectively the variations"
-              }
-          },
-      "GeneticDataType": {
-              "LongName": "GeneticDataType",
-              "Description": "Raw genetic data type submited for the dataset",
-              "Levels": {
-                  "WES": "Whole Exome Sequencing data (compressed FastQ or binary data format such as BAM or CRAM )",
-                  "SNP_intensity": "SNP array intensity data (text formated data type known as Illumina Final Report data)",
-                  "WES/SNP_intensity": "Both WES or SNP array data are available"
-              }
-        }
-  }
+{
+  "age": {
+    "LongName": "age",
+    "Description": "age of the participant",
+    "Units": "month"
+  },
+  "sex": {
+    "LongName": "sex",
+    "Description": "sex of the participant",
+    "Levels": {
+      "M": "male",
+      "F": "female"
+    }
+  },
+  "group": {
+    "LongName": "group",
+    "Description": "classification of participant based on study desease status",
+    "Levels": {
+      "patient": "patient",
+      "control": "control"
+    }
+  },
+  "genetic_id": {
+    "LongName": "genetic_id",
+    "Description": "Uniq sample ID per genotyped sample in genetic database"
+  },
+  "IDH": {
+    "LongName": "isocitrate dehydrogenase gene",
+    "Description": "mutation present or abscent",
+    "Levels": {
+      "yes": "present",
+      "no": "abscent"
+    }
+  },
+  "BatchID": {
+    "LongName": "BatchID",
+    "Description": "SNP array genotyping uniq batch ID per group of subjects",
+    "Levels": {
+      "b001": "Batch sequence number 1",
+      "b002": "Batch sequence number 2",
+      "b003": "Batch sequence number 3",
+      "b004": "Batch sequence number 4",
+      "b005": "Batch sequence number 5"
+    }
+  },
+  "VariationSetType": {
+    "LongName": "VariationSetType",
+    "Description": "Availability of SNV and/or CNV information",
+    "Levels": {
+      "SNV": "Single-nucleotide variants",
+      "CNV": "Copy-Number Variants",
+      "SNV/CNV": "Single-nucleotide variants/Copy-Number Variants"
+    }
+  },
+  "Assembly": {
+    "LongName": "Assembly",
+    "Description": "Reference genome from which the sample variations were computed",
+    "Levels": {
+      "hg19": "Human genome version 19 equivalent to GRCh37 (Genome Reference consorcium of human build 37)",
+      "hg38": "Human genome version 38 equivalent to GRCh38 (Genome Reference consorcium of human build 38)",
+      "hg19/hg38": "Genome used to compute respectively the variations"
+    }
+  },
+  "GeneticDataType": {
+    "LongName": "GeneticDataType",
+    "Description": "Raw genetic data type submited for the dataset",
+    "Levels": {
+      "WES": "Whole Exome Sequencing data (compressed FastQ or binary data format such as BAM or CRAM )",
+      "SNP_intensity": "SNP array intensity data (text formated data type known as Illumina Final Report data)",
+      "WES/SNP_intensity": "Both WES or SNP array data are available"
+    }
+  }
+}
diff --git a/mrs_fmrs/participants.json b/mrs_fmrs/participants.json
@@ -1,6 +1,6 @@
 {
   "participant_id": {
-      "Description": "Unique participant identifier"
+    "Description": "Unique participant identifier"
   },
   "sex": {
     "Description": "Sex of the participant",
@@ -10,7 +10,13 @@
     }
   },
   "age": {
-    "Description": "Age of the participant",
-    "Units": "years"
+    "Description": "Age of the participant, in 5-year intervals",
+    "Format": "string",
+    "Levels": {
+      "20-25": "20 to 25 years",
+      "25-30": "25 to 30 years",
+      "30-35": "30 to 35 years",
+      "35-40": "35 to 40 years"
+    }
   }
 }
diff --git a/pet002/participants.tsv b/pet002/participants.tsv
@@ -1,3 +1,3 @@
-participant_id	height	weight	age	gender
-sub-01	163.5	51	21.5086	female
-sub-02	170	51.2	20.7255	female
+participant_id	height	weight	age	gender
+sub-01	163.5	51	21.5086	F
+sub-02	170	51.2	20.7255	F
diff --git a/xeeg_hed_score/sub-ieegModulator/ses-ieeg01/ieeg/sub-ieegModulator_ses-ieeg01_electrodes.json b/xeeg_hed_score/sub-ieegModulator/ses-ieeg01/ieeg/sub-ieegModulator_ses-ieeg01_electrodes.json

Original file line number	Diff line number	Diff line change
`@@ -11,7 +11,8 @@`
`11`	`11`	`"Description": "Type of event (different from EEGLAB convention)",`
`12`	`12`	`"Levels": {`
`13`	`13`	`"stimulus": "Onset of first question",`
`14`		`- "response": "Response to question 1, 2 or 3"`
	`14`	`+ "response": "Response to question 1, 2 or 3",`
	`15`	`+ "STATUS": "Status event"`
`15`	`16`	`}`
`16`	`17`	`},`
`17`	`18`	`"response_time": {`
`@@ -27,7 +28,8 @@`
`27`	`28`	`"4": "Response 2 (this may be a response to question 1, 2 or 3)",`
`28`	`29`	`"8": "Response 3 (this may be a response to question 1, 2 or 3)",`
`29`	`30`	`"16": "Indicate involuntary response",`
`30`		`- "128": "First question onset (most important marker)"`
	`31`	`+ "128": "First question onset (most important marker)",`
	`32`	`+ "254": "Status event"`
`31`	`33`	`}`
`32`	`34`	`}`
`33`	`35`	`}`