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-HOSPA/README.md

@@ -0,0 +1,6 @@
+# Harvard-Oxford Subcortical Probabilistic Atlas
+
+This repository contains the Harvard-Oxford Subcortical Probabilistic Atlas (HOSPA) for the MNI152NLin6Asym and MNI152NLin2009cAsym templates,
+organized in BIDS format.
+
+The HOSPA atlas files were downloaded from TemplateFlow and do not match the files in https://github.com/HOA-2/SubcorticalParcellations.

atlas-HOSPA/tpl-MNI152NLin2009cAsym/atlas-HOSPA_description.json

@@ -0,0 +1,38 @@
+{
+    "Name": "Harvard-Oxford Subcortical Probabilistic Atlas",
+    "SampleSize": 200,
+    "SpatialReference": "",
+    "Description": "The Harvard-Oxford Atlas 2.0 project is developing a state-of-the-art, high-resolution full brain MR atlas consisting of 200 high definition MR data sets from the Human Connectome Project (HCP) parcellated into 392 gray and white matter PUs using structural MRI and 189 white matter fascicles using diffusion MRI. Manual parcellation will be performed based on a developed neuroanatomical ontology using a principled and well-defined parcellation methodology.",
+    "Authors": [
+        "R. Jarrett Rushmore",
+        "Kyle Sutherland",
+        "Holly Carrington",
+        "Justine Chen",
+        "Michael Halle",
+        "Andras Lasso",
+        "George Papadimitriou",
+        "Nick Prunier",
+        "Elizabeth Rizzoni",
+        "Brynn Vessey",
+        "Peter Wilson-Braun",
+        "Yogesh Rathi",
+        "Marek Kubicki",
+        "Sylvain Bouix",
+        "Edward Yeterian",
+        "Nikos Makris"
+    ],
+    "Curators": [
+        "Taylor Salo"
+    ],
+    "Funding": [
+        "NIH NIMH 5R01MH112748-04"
+    ],
+    "License": "https://raw.githubusercontent.com/Slicer/Slicer/main/License.txt",
+    "ReferencesAndLinks": [
+        "https://github.com/HOA-2/SubcorticalParcellations",
+        "https://cma.mgh.harvard.edu"
+    ],
+    "Species": "Human",
+    "DerivedFrom": "resting-state",
+    "LevelType": "group"
+}

atlas-HOSPA/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_atlas-HOSPA_dseg.tsv

@@ -0,0 +1,23 @@
+index	name	xyz
+0	Background	n/a
+1	Left Cerebral White Matter	58, 37, 50
+2	Left Cerebral Cortex 	70, 63, 35
+3	Left Lateral Ventrical	57, 40, 41
+4	Left Thalamus	51, 51, 39
+5	Left Caudate	51, 71, 38
+6	Left Putamen	56, 67, 34
+7	Left Pallidum	54, 62, 35
+8	Brainstem	44, 49, 18
+9	Left Hippocampus	59, 54, 27
+10	Left Amygdala	57, 61, 27
+11	Left Accumbens	50, 70, 33
+12	Right Cerebral White Matter	29, 38, 51
+13	Right Cerebral Cortex 	25, 42, 61
+14	Right Lateral Ventricle	35, 45, 44
+15	Right Thalamus	38, 51, 39
+16	Right Caudate	39, 72, 37
+17	Right Putamen	34, 68, 34
+18	Right Pallidum	35, 61, 35
+19	Right Hippocampus	31, 57, 25
+20	Right Amygdala	32, 63, 25
+21	Right Accumbens	40, 69, 32

atlas-HOSPA/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_atlas-HOSPA_probseg.tsv

@@ -0,0 +1,23 @@
+index	name	xyz
+0	Background	n/a
+1	Left Cerebral White Matter	58, 37, 50
+2	Left Cerebral Cortex 	70, 63, 35
+3	Left Lateral Ventrical	57, 40, 41
+4	Left Thalamus	51, 51, 39
+5	Left Caudate	51, 71, 38
+6	Left Putamen	56, 67, 34
+7	Left Pallidum	54, 62, 35
+8	Brainstem	44, 49, 18
+9	Left Hippocampus	59, 54, 27
+10	Left Amygdala	57, 61, 27
+11	Left Accumbens	50, 70, 33
+12	Right Cerebral White Matter	29, 38, 51
+13	Right Cerebral Cortex 	25, 42, 61
+14	Right Lateral Ventricle	35, 45, 44
+15	Right Thalamus	38, 51, 39
+16	Right Caudate	39, 72, 37
+17	Right Putamen	34, 68, 34
+18	Right Pallidum	35, 61, 35
+19	Right Hippocampus	31, 57, 25
+20	Right Amygdala	32, 63, 25
+21	Right Accumbens	40, 69, 32

atlas-HOSPA/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_atlas-HOSPA_dseg.json

@@ -0,0 +1,10 @@
+{
+    "SpatialReference": "https://templateflow.s3.amazonaws.com/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz",
+    "Manual": "true",
+    "CoordinateReportStrategy": "center_of_mass",
+    "Resolution": "1.0 x 1.0 x 1.0 mm",
+    "xyz": {
+        "Description": "XYZ coordinates of the centroid of the parcel",
+        "Delimiter": ", "
+    }
+}

atlas-HOSPA/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_atlas-HOSPA_probseg.json

@@ -0,0 +1,10 @@
+{
+    "SpatialReference": "https://templateflow.s3.amazonaws.com/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz",
+    "Manual": "true",
+    "CoordinateReportStrategy": "center_of_mass",
+    "Resolution": "1.0 x 1.0 x 1.0 mm",
+    "xyz": {
+        "Description": "XYZ coordinates of the centroid of the parcel",
+        "Delimiter": ", "
+    }
+}

atlas-HOSPA/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_atlas-HOSPA_dseg.json

@@ -0,0 +1,10 @@
+{
+    "SpatialReference": "https://templateflow.s3.amazonaws.com/tpl-MNI152NLin2009cAsym_res-02_T1w.nii.gz",
+    "Manual": "true",
+    "CoordinateReportStrategy": "center_of_mass",
+    "Resolution": "2.0 x 2.0 x 2.0 mm",
+    "xyz": {
+        "Description": "XYZ coordinates of the centroid of the parcel",
+        "Delimiter": ", "
+    }
+}

atlas-HOSPA/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_atlas-HOSPA_probseg.json

@@ -0,0 +1,10 @@
+{
+    "SpatialReference": "https://templateflow.s3.amazonaws.com/tpl-MNI152NLin2009cAsym_res-02_T1w.nii.gz",
+    "Manual": "true",
+    "CoordinateReportStrategy": "center_of_mass",
+    "Resolution": "2.0 x 2.0 x 2.0 mm",
+    "xyz": {
+        "Description": "XYZ coordinates of the centroid of the parcel",
+        "Delimiter": ", "
+    }
+}

atlas-HOSPA/tpl-MNI152NLin6Asym/atlas-HOSPA_description.json

@@ -0,0 +1,38 @@
+{
+    "Name": "Harvard-Oxford Subcortical Probabilistic Atlas",
+    "SampleSize": 200,
+    "SpatialReference": "",
+    "Description": "The Harvard-Oxford Atlas 2.0 project is developing a state-of-the-art, high-resolution full brain MR atlas consisting of 200 high definition MR data sets from the Human Connectome Project (HCP) parcellated into 392 gray and white matter PUs using structural MRI and 189 white matter fascicles using diffusion MRI. Manual parcellation will be performed based on a developed neuroanatomical ontology using a principled and well-defined parcellation methodology.",
+    "Authors": [
+        "R. Jarrett Rushmore",
+        "Kyle Sutherland",
+        "Holly Carrington",
+        "Justine Chen",
+        "Michael Halle",
+        "Andras Lasso",
+        "George Papadimitriou",
+        "Nick Prunier",
+        "Elizabeth Rizzoni",
+        "Brynn Vessey",
+        "Peter Wilson-Braun",
+        "Yogesh Rathi",
+        "Marek Kubicki",
+        "Sylvain Bouix",
+        "Edward Yeterian",
+        "Nikos Makris"
+    ],
+    "Curators": [
+        "Taylor Salo"
+    ],
+    "Funding": [
+        "NIH NIMH 5R01MH112748-04"
+    ],
+    "License": "https://raw.githubusercontent.com/Slicer/Slicer/main/License.txt",
+    "ReferencesAndLinks": [
+        "https://github.com/HOA-2/SubcorticalParcellations",
+        "https://cma.mgh.harvard.edu"
+    ],
+    "Species": "Human",
+    "DerivedFrom": "resting-state",
+    "LevelType": "group"
+}

atlas-HOSPA/tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_atlas-HOSPA_dseg.tsv

@@ -0,0 +1,23 @@
+index	name	xyz
+0	Background	n/a
+1	Left Cerebral White Matter	58, 37, 50
+2	Left Cerebral Cortex 	70, 63, 35
+3	Left Lateral Ventrical	57, 40, 41
+4	Left Thalamus	51, 51, 39
+5	Left Caudate	51, 71, 38
+6	Left Putamen	56, 67, 34
+7	Left Pallidum	54, 62, 35
+8	Brainstem	44, 49, 18
+9	Left Hippocampus	59, 54, 27
+10	Left Amygdala	57, 61, 27
+11	Left Accumbens	50, 70, 33
+12	Right Cerebral White Matter	29, 38, 51
+13	Right Cerebral Cortex 	25, 42, 61
+14	Right Lateral Ventricle	35, 45, 44
+15	Right Thalamus	38, 51, 39
+16	Right Caudate	39, 72, 37
+17	Right Putamen	34, 68, 34
+18	Right Pallidum	35, 61, 35
+19	Right Hippocampus	31, 57, 25
+20	Right Amygdala	32, 63, 25
+21	Right Accumbens	40, 69, 32

atlas-HOSPA/tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_atlas-HOSPA_probseg.tsv

@@ -0,0 +1,23 @@
+index	name	xyz
+0	Background	n/a
+1	Left Cerebral White Matter	58, 37, 50
+2	Left Cerebral Cortex 	70, 63, 35
+3	Left Lateral Ventrical	57, 40, 41
+4	Left Thalamus	51, 51, 39
+5	Left Caudate	51, 71, 38
+6	Left Putamen	56, 67, 34
+7	Left Pallidum	54, 62, 35
+8	Brainstem	44, 49, 18
+9	Left Hippocampus	59, 54, 27
+10	Left Amygdala	57, 61, 27
+11	Left Accumbens	50, 70, 33
+12	Right Cerebral White Matter	29, 38, 51
+13	Right Cerebral Cortex 	25, 42, 61
+14	Right Lateral Ventricle	35, 45, 44
+15	Right Thalamus	38, 51, 39
+16	Right Caudate	39, 72, 37
+17	Right Putamen	34, 68, 34
+18	Right Pallidum	35, 61, 35
+19	Right Hippocampus	31, 57, 25
+20	Right Amygdala	32, 63, 25
+21	Right Accumbens	40, 69, 32

atlas-HOSPA/tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-01_atlas-HOSPA_dseg.json

@@ -0,0 +1,10 @@
+{
+    "SpatialReference": "https://templateflow.s3.amazonaws.com/tpl-MNI152NLin6Asym_res-01_T1w.nii.gz",
+    "Manual": "true",
+    "CoordinateReportStrategy": "center_of_mass",
+    "Resolution": "1.0 x 1.0 x 1.0 mm",
+    "xyz": {
+        "Description": "XYZ coordinates of the centroid of the parcel",
+        "Delimiter": ", "
+    }
+}

atlas-HOSPA/tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-01_atlas-HOSPA_probseg.json

@@ -0,0 +1,10 @@
+{
+    "SpatialReference": "https://templateflow.s3.amazonaws.com/tpl-MNI152NLin6Asym_res-01_T1w.nii.gz",
+    "Manual": "true",
+    "CoordinateReportStrategy": "center_of_mass",
+    "Resolution": "1.0 x 1.0 x 1.0 mm",
+    "xyz": {
+        "Description": "XYZ coordinates of the centroid of the parcel",
+        "Delimiter": ", "
+    }
+}

atlas-HOSPA/tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-02_atlas-HOSPA_dseg.json

@@ -0,0 +1,10 @@
+{
+    "SpatialReference": "https://templateflow.s3.amazonaws.com/tpl-MNI152NLin6Asym_res-02_T1w.nii.gz",
+    "Manual": "true",
+    "CoordinateReportStrategy": "center_of_mass",
+    "Resolution": "2.0 x 2.0 x 2.0 mm",
+    "xyz": {
+        "Description": "XYZ coordinates of the centroid of the parcel",
+        "Delimiter": ", "
+    }
+}

atlas-HOSPA/tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-02_atlas-HOSPA_probseg.json

@@ -0,0 +1,10 @@
+{
+    "SpatialReference": "https://templateflow.s3.amazonaws.com/tpl-MNI152NLin6Asym_res-02_T1w.nii.gz",
+    "Manual": "true",
+    "CoordinateReportStrategy": "center_of_mass",
+    "Resolution": "2.0 x 2.0 x 2.0 mm",
+    "xyz": {
+        "Description": "XYZ coordinates of the centroid of the parcel",
+        "Delimiter": ", "
+    }
+}

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])