BEP038: Atlas examples

.github/workflows/validate_datasets.yml

@@ -2,12 +2,10 @@ name: validate_datasets
 
 on:
   push:
-    branches: ['**']
+    branches: [master, main]
+    tags: ['*']
   pull_request:
-    branches: ['**']
-  create:
-    branches: [master]
-    tags: ['**']
+    branches: [master, main, 'bep*']
   schedule:
     - cron: "0 4 * * 1"
 
@@ -95,7 +93,7 @@ jobs:
         fi
 
     - name: Skip legacy validation for post-legacy datasets
-      run: for DS in mrs_* dwi_deriv pheno004; do touch $DS/.SKIP_VALIDATION; done
+      run: for DS in mrs_* dwi_deriv pheno004 atlas-*; do touch $DS/.SKIP_VALIDATION; done
       if: matrix.bids-validator == 'legacy'
 
     - name: Skip stable validation for datasets with unreleased validator features
@@ -107,7 +105,7 @@ 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 dwi_deriv pheno004 atlas-*; do touch $DS/.SKIP_VALIDATION; done
       if: matrix.bids-validator != 'dev'
 
     - name: Set BIDS_SCHEMA variable for dev version
@@ -116,7 +114,7 @@ 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--1714.org.readthedocs.build/en/1714/schema.json >> $GITHUB_ENV
 
     - name: Validate all BIDS datasets using bids-validator
       run: |

atlas-suit/atlas-Buckner2011_description.json

@@ -0,0 +1,18 @@
+{
+    "Name": "The organization of the human cerebellum estimated by intrinsic functional connectivity",
+    "Authors": [
+        "Randy L Buckner",
+        "Fenna M Krienen",
+        "Angela Castellanos",
+        "Julio C Diaz",
+        "B T Thomas Yeo"
+    ],
+    "SampleSize": 1000,
+    "SpatialReference": "https://templateflow.s3.amazonaws.com/tpl-MNI152Lin_res-01_T1w.nii.gz",
+    "License": "LICENSE file",
+    "ReferencesAndLinks": [
+        "https://doi.org/10.1152/jn.00339.2011",
+        "https://github.com/jdiedrichsen/suit"
+    ],
+    "Species": "Human"
+}

atlas-suit/atlas-Diedrichsen2009_description.json

@@ -0,0 +1,18 @@
+{
+    "Name": "A probabilistic MR atlas of the human cerebellum",
+    "Authors": [
+        "Jörn Diedrichsen",
+        "Joshua H Balsters",
+        "Jonathan Flavell",
+        "Emma Cussans",
+        "Narender Ramnani"
+    ],
+    "SampleSize": 20,
+    "SpatialReference": "https://templateflow.s3.amazonaws.com/tpl-MNI152Lin_res-01_T1w.nii.gz",
+    "License": "LICENSE file",
+    "ReferencesAndLinks": [
+        "https://doi.org/10.1016/j.neuroimage.2009.01.045",
+        "https://github.com/jdiedrichsen/suit"
+    ],
+    "Species": "Human"
+}

atlas-suit/dataset_description.json

@@ -0,0 +1,11 @@
+{
+    "Name": "The SUIT Atlas",
+    "BIDSVersion": "1.11.0",
+    "DatasetType": "derivative",
+    "GeneratedBy": [
+        {
+            "Name": "Manual",
+            "Description": "Curation of SUIT atlas into BIDS format"
+        }
+    ]
+}

atlas-suit/tpl-SUIT/anat/tpl-SUIT_T1w.json

@@ -0,0 +1,3 @@
+{
+    "SkullStripped": true
+}

atlas-suit/tpl-SUIT/anat/tpl-SUIT_atlas-Diedrichsen2009_dseg.json

@@ -0,0 +1,3 @@
+{
+
+}

atlas-suit/tpl-SUIT/anat/tpl-SUIT_atlas-Diedrichsen2009_dseg.tsv

@@ -0,0 +1,35 @@
+index	name	color
+1	Left_I_IV	#ccff00
+2	Right_I_IV	#b8e600
+3	Left_V	#00e65c
+4	Right_V	#00ff66
+5	Left_VI	#0066ff
+6	Vermis_VI	#0052cc
+7	Right_VI	#0066ff
+8	Left_CrusI	#cc00ff
+9	Vermis_CrusI	#a200cc
+10	Right_CrusI	#cc00ff
+11	Left_CrusII	#ff0000
+12	Vermis_CrusII	#cc0000
+13	Right_CrusII	#ff0000
+14	Left_VIIb	#ff9900
+15	Vermis_VIIb	#cc7900
+16	Right_VIIb	#ff9900
+17	Left_VIIIa	#33ff00
+18	Vermis_VIIIa	#29cc00
+19	Right_VIIIa	#33ff00
+20	Left_VIIIb	#00ffff
+21	Vermis_VIIIb	#00cccc
+22	Right_VIIIb	#00ffff
+23	Left_IX	#3300ff
+24	Vermis_IX	#2900cc
+25	Right_IX	#3300ff
+26	Left_X	#ff0099
+27	Vermis_X	#cc0079
+28	Right_X	#ff0099
+29	Left_Dentate	#4c4c4c
+30	Right_Dentate	#4c4c4c
+31	Left_Interposed	#7f7f7f
+32	Right_Interposed	#7f7f7f
+33	Left_Fastigial	#b2b2b2
+34	Right_Fastigial	#b2b2b2