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"
 
@@ -107,7 +105,7 @@ jobs:
         fi
 
     - name: Skip legacy validation for post-legacy datasets
-      run: for DS in mrs_* dwi_deriv pet006 pheno004 volume_timing; do touch $DS/.SKIP_VALIDATION; done
+      run: for DS in mrs_* dwi_deriv pet006 pheno004 volume_timing atlas-*; do touch $DS/.SKIP_VALIDATION; done
       if: matrix.bids-validator == 'legacy'
 
     - name: Skip stable validation for datasets with unreleased validator features
@@ -119,7 +117,7 @@ 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
@@ -128,7 +126,7 @@ 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-ONPNeuroMarkflorbetapir/README.txt

@@ -0,0 +1,50 @@
+Florbetapir NeuroMark Independent Component Analysis Atlas (MNI305 Space, 2 mm)
+================================================================================
+
+Overview
+--------
+This dataset contains an Independent Component Analysis (ICA)-based PET atlas constructed from cognitively normal subjects in the Alzheimer's Disease Neuroimaging Initiative (ADNI). The atlas was generated using the NeuroMark PET ICA pipeline.
+
+Data were derived from 296 subjects with 18F-florbetapir PET scans, SUVR-normalized using the whole cerebellum as the reference region, and resampled to MNI305 space at 2 mm isotropic resolution. ICA was performed using a model order of 40, resulting in 19 spatial components: 17 amyloid-beta networks and 2 cerebellar components.
+
+Contents
+--------
+- dataset_description.json: BIDS metadata describing the dataset, authorship, funding, and citation.
+- atlas-ADNINeuroMarkflorbetapir_description.json: Metadata for this specific atlas.
+- descriptions.tsv: Tabular listing of the ICA components and their functional labels.
+- pet/tpl-PETprep_space-MNI305_atlas-ADNINeuroMarkflorbetapir_res-2_desc-ICN_pet.nii.gz: The atlas image file in PET modality, Z-scored.
+
+File Naming Convention
+-----------------------
+The atlas file follows BIDS derivative naming:
+  tpl-PETprep_space-MNI305_atlas-ADNINeuroMarkflorbetapir_res-2_desc-ICN_pet.nii.gz
+
+Where:
+- tpl-PETprep: Indicates this is a PET template.
+- space-MNI305: Registered to MNI305 standard space.
+- atlas-ADNINeuroMarkflorbetapir: Describes the source and method of atlas creation.
+- res-2: 2 mm isotropic resolution.
+- desc-ICA: Denotes Independent Component Analysis-derived components.
+
+Source Data
+-----------
+All subjects were selected from the ADNI GO/2/3 phases. Raw PET data were acquired using four 5-minute frames per subject and processed using standard SUVR normalization with the whole cerebellum as reference.
+
+Please refer to the ADNI website for data access policies:
+http://adni.loni.usc.edu
+
+Acknowledgment
+--------------
+If you use this dataset, please cite the following publication:
+
+Eierud C, et al. (2025). *Building Multivariate Molecular Imaging Brain Atlases Using the NeuroMark PET Independent Component Analysis Framework*. Aperture Neuro. https://doi.org/10.52294/001c.142578
+
+Please also cite the Alzheimer's Disease Neuroimaging Initiative (ADNI) and acknowledge their funding sources as described at: http://adni.loni.usc.edu
+
+License
+-------
+This dataset is distributed under the Creative Commons Attribution 4.0 International License (CC-BY-4.0).
+
+Contact
+-------
+For questions or issues, please contact Cyrus Eierud ([email protected])

atlas-ONPNeuroMarkflorbetapir/dataset_description.json

@@ -0,0 +1,40 @@
+{
+  "Name": "OpenNeuroPET NeuroMark Florbetaben Atlas",
+  "BIDSVersion": "1.10.1",
+  "DatasetType": "derivative", 
+  "Description": "Atlas consisting of 17 amyloid-beta networks and 2 cerebellar independent component networks, derived from 18F-florbetapir PET imaging using four 5-minute frames per subject, having been SUVR normalized, using the whole cerebellum as reference. The altas follows the publication titled Building Multivariate Molecular Imaging Brain Atlases Using the NeuroMark PET Independent Component Analysis Framework. Authors for publication are the same as in the Authors tag in this json file. ICA processing used model order 40 and 296 florbetapir subjects (mean=76.1 years, SD=8.0 years)",
+  "Authors": [
+    "Cyrus Eierud",
+    "Martin Norgaard",
+    "Murat Bilgel",
+    "Helen Petropoulos",
+    "Zening Fu",
+    "Armin Iraji",
+    "Granville J. Matheson",
+    "Melanie Ganz",
+    "Cyril Pernet",
+    "Vince D. Calhoun",
+    "The Alzheimer’s Disease Neuroimaging Initiative"
+  ],
+  "Funding": [
+	"National Institutes of Health (NIH), Grant U01AG024904",
+    "U.S. Department of Defense, Grant W81XWH-12-2-0012",
+    "National Science Foundation (NSI), Grant 2112455",
+    "National Institutes of Health (NIH), Grant RF1AG063153",
+    "Vetenskapsrådet, Grant 2020-06356",
+    "National Institute on Aging (NIA), Intramural Research Program Grant",
+    "Novo Nordisk Fonden, Grant NN20OC0063277",
+    "BRAIN Initiative, Grant 1R24MH120004-01A1"
+  ],
+  "SourceDatasets": [
+    {
+        "URL": "http://adni.loni.usc.edu",
+        "Name": "Alzheimer’s Disease Neuroimaging Initiative (ADNI)",
+        "Version": "ADNI GO/2/3"
+    }
+  ],
+  "HowToAcknowledge": "Please acknowledge this dataset by citing the publication: Eierud C, et al. 'Building Multivariate Molecular Imaging Brain Atlases Using the NeuroMark PET Independent Component Analysis Framework.' Aperture Neuro, 2025. doi:10.52294/001c.142578",
+  "Species": "Human",
+  "License": "CC-BY-4.0",
+  "ReferencesAndLinks": ["https://doi.org/10.52294/001c.142578"]
+}

atlas-ONPNeuroMarkflorbetapir/tpl-PETprep/atlas-ONPNeuroMarkflorbetapir_description.json

@@ -0,0 +1,46 @@
+{
+  "Name": "OpenNeuroPET NeuroMark Florbetaben Atlas",
+  "BIDSVersion": "1.10.1",
+  "Description": "Atlas consisting of 17 amyloid-beta independent component networks and 2 cerebellar independent component networks, derived from 18F-florbetapir PET imaging using four 5-minute frames per subject, having been SUVR normalized, using the whole cerebellum as reference. The altas follows the publication titled Building Multivariate Molecular Imaging Brain Atlases Using the NeuroMark PET Independent Component Analysis Framework. Authors for publication are the same as in the Authors tag in this json file. ICA processing used model order 40 and 296 florbetapir subjects (mean=76.1 years, SD=8.0 years)",
+  "Modality": "PET",
+  "TracerName": "Florbetapir",
+  "Units": "Z-scores",
+  "SpatialReference": "MNI305",
+  "Resolution": "2mm",
+  "LevelType": "group",
+  "SampleSize": 296,
+  "MeanAge": 76.1,
+  "AgeSD": 8.0,
+  "GroupDescription": "Cognitively normal",
+  "AtlasType": "NeuroMark independent component networks (ICNs)",
+  "SpatialMaps": [
+    { "Index": 1, "Label": "AU1", "Description": "Auditory Network 1" },
+    { "Index": 2, "Label": "AU2", "Description": "Auditory Network 2" },
+    { "Index": 3, "Label": "SM1", "Description": "Somatosensory Network 1" },
+    { "Index": 4, "Label": "SM2", "Description": "Somatosensory Network 2" },
+    { "Index": 5, "Label": "SM3", "Description": "Somatosensory Network 3" },
+    { "Index": 6, "Label": "VI1", "Description": "Visual Network 1" },
+    { "Index": 7, "Label": "VI2", "Description": "Visual Network 2" },
+    { "Index": 8, "Label": "VI3", "Description": "Visual Network 3" },
+    { "Index": 9, "Label": "VI4", "Description": "Visual Network 4" },
+    { "Index": 10, "Label": "VI5", "Description": "Visual Network 5" },
+    { "Index": 11, "Label": "CC1", "Description": "Cognitive Control Network 1" },
+    { "Index": 12, "Label": "CC2", "Description": "Cognitive Control Network 2" },
+    { "Index": 13, "Label": "CC3", "Description": "Cognitive Control Network 3" },
+    { "Index": 14, "Label": "DM1", "Description": "Default Mode Network 1" },
+    { "Index": 15, "Label": "DM2", "Description": "Default Mode Network 2" },
+    { "Index": 16, "Label": "DM3", "Description": "Default Mode Network 3" },
+    { "Index": 17, "Label": "DM4", "Description": "Default Mode Network 4" },
+    { "Index": 18, "Label": "CB1", "Description": "Cerebellum Network 1" },
+    { "Index": 19, "Label": "CB2", "Description": "Cerebellum Network 2" }
+  ],
+  "License": "CC-BY-4.0",
+  "ReferencesAndLinks": ["https://doi.org/10.52294/001c.142578"],
+  "SourceDatasets": [
+	{
+		"URL": "http://adni.loni.usc.edu",
+		"Name": "Alzheimer’s Disease Neuroimaging Initiative (ADNI)",
+		"Version": "ADNI GO/2/3"
+	}
+  ]
+}

atlas-ONPNeuroMarkflorbetapir/tpl-PETprep/descriptions.tsv

@@ -0,0 +1,2 @@
+desc_id	description
+ICN	indepedent component networks (see json file for index and network names)

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