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-4S/README.md

@@ -0,0 +1,8 @@
+# 4S: Schaefer Supplemented with Subcortical Structures
+
+This repository contains two resolutions (156, 256) of the 4S atlas,
+which is the Schaefer 2018 cortical atlas supplemented with subcortical structures from other atlases.
+
+The atlas is shared in MNI152NLin6Asym, MNI152NLin2009cAsym, MNIInfant:cohort-1, MNIInfant:cohort-2, and fsLR space.
+
+There are also versions of the atlas warped to subject-specific spaces and/or resolutions in the `sub-<label>` directories.

atlas-4S/dataset_description.json

@@ -0,0 +1,5 @@
+{
+    "BIDSVersion": "1.11.0",
+    "DatasetType": "derivative",
+    "Name": "4S: Schaefer Supplemented with Subcortical Structures"
+}

atlas-4S/sub-01/ses-2mo/anat/sub-01_ses-2mo_space-MNIInfant+1_atlas-4S_scale-156_dseg.json

@@ -0,0 +1,24 @@
+{
+    "Manual": "false",
+    "Sources": [
+        "bids::tpl-MNIInfant/cohort-1/anat/tpl-MNIInfant_cohort-1_atlas-4S_scale-156_res-01_dseg.nii.gz",
+        "bids::sub-01/ses-2mo/anat/sub-01_ses-2mo_space-MNIInfant+1_desc-preproc_T1w.nii.gz"
+    ],
+    "SpatialReference": "https://templateflow.s3.amazonaws.com/tpl-MNIInfant_cohort-1_res-1_T1w.nii.gz",
+    "index_17network": {
+        "Description": "The corresponding integer value of this node in the 17-network Schaefer atlas imaging file.",
+        "LongName": "Node index from Schaefer 17-network atlas"
+    },
+    "name_17network": {
+        "Description": "The label of the node as it appears in the canonical Schaefer 17-network atlas.",
+        "LongName": "Node label from Schaefer 17-network atlas"
+    },
+    "name_7network": {
+        "Description": "The label of the node as it appears in the canonical Schaefer 7-network atlas.",
+        "LongName": "Node label from Schaefer 7-network atlas"
+    },
+    "network_label_17network": {
+        "Description": "The name of the network this node is assigned to in the Schaefer 17-network atlas.",
+        "LongName": "Network label from Schaefer 17-network atlas"
+    }
+}

atlas-4S/sub-01/ses-2mo/anat/sub-01_ses-2mo_space-MNIInfant+1_atlas-4S_scale-256_dseg.json

@@ -0,0 +1,24 @@
+{
+    "Manual": "false",
+    "Sources": [
+        "bids::tpl-MNIInfant/cohort-1/anat/tpl-MNIInfant_cohort-1_atlas-4S_scale-256_res-01_dseg.nii.gz",
+        "bids::sub-01/ses-2mo/anat/sub-01_ses-2mo_space-MNIInfant+1_desc-preproc_T1w.nii.gz"
+    ],
+    "SpatialReference": "https://templateflow.s3.amazonaws.com/tpl-MNIInfant_cohort-1_res-1_T1w.nii.gz",
+    "index_17network": {
+        "Description": "The corresponding integer value of this node in the 17-network Schaefer atlas imaging file.",
+        "LongName": "Node index from Schaefer 17-network atlas"
+    },
+    "name_17network": {
+        "Description": "The label of the node as it appears in the canonical Schaefer 17-network atlas.",
+        "LongName": "Node label from Schaefer 17-network atlas"
+    },
+    "name_7network": {
+        "Description": "The label of the node as it appears in the canonical Schaefer 7-network atlas.",
+        "LongName": "Node label from Schaefer 7-network atlas"
+    },
+    "network_label_17network": {
+        "Description": "The name of the network this node is assigned to in the Schaefer 17-network atlas.",
+        "LongName": "Network label from Schaefer 17-network atlas"
+    }
+}

atlas-4S/sub-01/ses-2mo/anat/sub-01_ses-2mo_space-MNIInfant+1_desc-preproc_T1w.json

@@ -0,0 +1,7 @@
+{
+    "SkullStripped": false,
+    "Sources": [
+        "bids::sub-01/ses-2mo/anat/sub-01_ses-2mo_desc-preproc_T1w.nii.gz"
+    ],
+    "SpatialReference": "https://templateflow.s3.amazonaws.com/tpl-MNIInfant_cohort-1_res-1_T1w.nii.gz"
+}

atlas-4S/sub-01/ses-2mo/anat/sub-01_ses-2mo_space-MNIInfant+2_atlas-4S_scale-156_dseg.json

@@ -0,0 +1,24 @@
+{
+    "Manual": "false",
+    "Sources": [
+        "bids::tpl-MNIInfant/cohort-2/anat/tpl-MNIInfant_cohort-2_atlas-4S_scale-156_res-01_dseg.nii.gz",
+        "bids::sub-01/ses-2mo/anat/sub-01_ses-2mo_space-MNIInfant+2_desc-preproc_T1w.nii.gz"
+    ],
+    "SpatialReference": "https://templateflow.s3.amazonaws.com/tpl-MNIInfant_cohort-2_res-01_T1w.nii.gz",
+    "index_17network": {
+        "Description": "The corresponding integer value of this node in the 17-network Schaefer atlas imaging file.",
+        "LongName": "Node index from Schaefer 17-network atlas"
+    },
+    "name_17network": {
+        "Description": "The label of the node as it appears in the canonical Schaefer 17-network atlas.",
+        "LongName": "Node label from Schaefer 17-network atlas"
+    },
+    "name_7network": {
+        "Description": "The label of the node as it appears in the canonical Schaefer 7-network atlas.",
+        "LongName": "Node label from Schaefer 7-network atlas"
+    },
+    "network_label_17network": {
+        "Description": "The name of the network this node is assigned to in the Schaefer 17-network atlas.",
+        "LongName": "Network label from Schaefer 17-network atlas"
+    }
+}

atlas-4S/sub-01/ses-2mo/anat/sub-01_ses-2mo_space-MNIInfant+2_atlas-4S_scale-256_dseg.json

@@ -0,0 +1,24 @@
+{
+    "Manual": "false",
+    "Sources": [
+        "bids::tpl-MNIInfant/cohort-2/anat/tpl-MNIInfant_cohort-2_atlas-4S_scale-256_res-01_dseg.nii.gz",
+        "bids::sub-01/ses-2mo/anat/sub-01_ses-2mo_space-MNIInfant+2_desc-preproc_T1w.nii.gz"
+    ],
+    "SpatialReference": "https://templateflow.s3.amazonaws.com/tpl-MNIInfant_cohort-2_res-01_T1w.nii.gz",
+    "index_17network": {
+        "Description": "The corresponding integer value of this node in the 17-network Schaefer atlas imaging file.",
+        "LongName": "Node index from Schaefer 17-network atlas"
+    },
+    "name_17network": {
+        "Description": "The label of the node as it appears in the canonical Schaefer 17-network atlas.",
+        "LongName": "Node label from Schaefer 17-network atlas"
+    },
+    "name_7network": {
+        "Description": "The label of the node as it appears in the canonical Schaefer 7-network atlas.",
+        "LongName": "Node label from Schaefer 7-network atlas"
+    },
+    "network_label_17network": {
+        "Description": "The name of the network this node is assigned to in the Schaefer 17-network atlas.",
+        "LongName": "Network label from Schaefer 17-network atlas"
+    }
+}

atlas-4S/sub-01/ses-2mo/anat/sub-01_ses-2mo_space-MNIInfant+2_desc-preproc_T1w.json

@@ -0,0 +1,7 @@
+{
+    "SkullStripped": false,
+    "Sources": [
+        "bids::sub-01/ses-2mo/anat/sub-01_ses-2mo_desc-preproc_T1w.nii.gz"
+    ],
+    "SpatialReference": "https://templateflow.s3.amazonaws.com/tpl-MNIInfant_cohort-2_res-01_T1w.nii.gz"
+}

atlas-4S/sub-01/ses-2mo/anat/sub-01_ses-2mo_space-anat_atlas-4S_scale-156_dseg.json

@@ -0,0 +1,24 @@
+{
+    "Manual": "false",
+    "Sources": [
+        "bids::tpl-MNIInfant/cohort-1/anat/tpl-MNIInfant_cohort-1_atlas-4S_scale-156_res-01_dseg.nii.gz",
+        "bids::sub-01/ses-2mo/anat/sub-01_ses-2mo_space-anat_desc-preproc_T1w.nii.gz"
+    ],
+    "SpatialReference": "bids::sub-01/ses-2mo/anat/sub-01_ses-2mo_space-anat_desc-preproc_T1w.nii.gz",
+    "index_17network": {
+        "Description": "The corresponding integer value of this node in the 17-network Schaefer atlas imaging file.",
+        "LongName": "Node index from Schaefer 17-network atlas"
+    },
+    "name_17network": {
+        "Description": "The label of the node as it appears in the canonical Schaefer 17-network atlas.",
+        "LongName": "Node label from Schaefer 17-network atlas"
+    },
+    "name_7network": {
+        "Description": "The label of the node as it appears in the canonical Schaefer 7-network atlas.",
+        "LongName": "Node label from Schaefer 7-network atlas"
+    },
+    "network_label_17network": {
+        "Description": "The name of the network this node is assigned to in the Schaefer 17-network atlas.",
+        "LongName": "Network label from Schaefer 17-network atlas"
+    }
+}

atlas-4S/sub-01/ses-2mo/anat/sub-01_ses-2mo_space-anat_atlas-4S_scale-256_dseg.json

@@ -0,0 +1,24 @@
+{
+    "Manual": "false",
+    "Sources": [
+        "bids::tpl-MNIInfant/cohort-1/anat/tpl-MNIInfant_cohort-1_atlas-4S_scale-256_res-01_dseg.nii.gz",
+        "bids::sub-01/ses-2mo/anat/sub-01_ses-2mo_space-anat_desc-preproc_T1w.nii.gz"
+    ],
+    "SpatialReference": "bids::sub-01/ses-2mo/anat/sub-01_ses-2mo_space-anat_desc-preproc_T1w.nii.gz",
+    "index_17network": {
+        "Description": "The corresponding integer value of this node in the 17-network Schaefer atlas imaging file.",
+        "LongName": "Node index from Schaefer 17-network atlas"
+    },
+    "name_17network": {
+        "Description": "The label of the node as it appears in the canonical Schaefer 17-network atlas.",
+        "LongName": "Node label from Schaefer 17-network atlas"
+    },
+    "name_7network": {
+        "Description": "The label of the node as it appears in the canonical Schaefer 7-network atlas.",
+        "LongName": "Node label from Schaefer 7-network atlas"
+    },
+    "network_label_17network": {
+        "Description": "The name of the network this node is assigned to in the Schaefer 17-network atlas.",
+        "LongName": "Network label from Schaefer 17-network atlas"
+    }
+}

atlas-4S/sub-01/ses-2mo/anat/sub-01_ses-2mo_space-anat_desc-preproc_T1w.json

@@ -0,0 +1,6 @@
+{
+    "SkullStripped": false,
+    "Sources": [
+        "bids:raw:sub-01/ses-2mo/anat/sub-01_ses-2mo_T1w.nii.gz"
+    ]
+}

atlas-4S/sub-01/ses-2mo/func/sub-01_ses-2mo_space-MNIInfant+1_atlas-4S_scale-156_dseg.json

@@ -0,0 +1,24 @@
+{
+    "Manual": "false",
+    "Sources": [
+        "bids::tpl-MNIInfant/cohort-2/anat/tpl-MNIInfant_cohort-1_atlas-4S_scale-156_res-01_dseg.nii.gz",
+        "bids::sub-01/ses-2mo/func/sub-01_ses-2mo_task-rest_space-MNIInfant+1_desc-preproc_bold.nii.gz"
+    ],
+    "SpatialReference": "https://templateflow.s3.amazonaws.com/tpl-MNIInfant_cohort-1_res-1_T1w.nii.gz",
+    "index_17network": {
+        "Description": "The corresponding integer value of this node in the 17-network Schaefer atlas imaging file.",
+        "LongName": "Node index from Schaefer 17-network atlas"
+    },
+    "name_17network": {
+        "Description": "The label of the node as it appears in the canonical Schaefer 17-network atlas.",
+        "LongName": "Node label from Schaefer 17-network atlas"
+    },
+    "name_7network": {
+        "Description": "The label of the node as it appears in the canonical Schaefer 7-network atlas.",
+        "LongName": "Node label from Schaefer 7-network atlas"
+    },
+    "network_label_17network": {
+        "Description": "The name of the network this node is assigned to in the Schaefer 17-network atlas.",
+        "LongName": "Network label from Schaefer 17-network atlas"
+    }
+}

atlas-4S/sub-01/ses-2mo/func/sub-01_ses-2mo_space-MNIInfant+1_atlas-4S_scale-256_dseg.json

@@ -0,0 +1,24 @@
+{
+    "Manual": "false",
+    "Sources": [
+        "bids::tpl-MNIInfant/cohort-2/anat/tpl-MNIInfant_cohort-1_atlas-4S_scale-256_res-01_dseg.nii.gz",
+        "bids::sub-01/ses-2mo/func/sub-01_ses-2mo_task-rest_space-MNIInfant+1_desc-preproc_bold.nii.gz"
+    ],
+    "SpatialReference": "https://templateflow.s3.amazonaws.com/tpl-MNIInfant_cohort-1_res-1_T1w.nii.gz",
+    "index_17network": {
+        "Description": "The corresponding integer value of this node in the 17-network Schaefer atlas imaging file.",
+        "LongName": "Node index from Schaefer 17-network atlas"
+    },
+    "name_17network": {
+        "Description": "The label of the node as it appears in the canonical Schaefer 17-network atlas.",
+        "LongName": "Node label from Schaefer 17-network atlas"
+    },
+    "name_7network": {
+        "Description": "The label of the node as it appears in the canonical Schaefer 7-network atlas.",
+        "LongName": "Node label from Schaefer 7-network atlas"
+    },
+    "network_label_17network": {
+        "Description": "The name of the network this node is assigned to in the Schaefer 17-network atlas.",
+        "LongName": "Network label from Schaefer 17-network atlas"
+    }
+}

atlas-4S/sub-01/ses-2mo/func/sub-01_ses-2mo_space-MNIInfant+2_atlas-4S_scale-156_dseg.json

@@ -0,0 +1,24 @@
+{
+    "Manual": "false",
+    "Sources": [
+        "bids::tpl-MNIInfant/cohort-2/anat/tpl-MNIInfant_cohort-2_atlas-4S_scale-156_res-01_dseg.nii.gz",
+        "bids::sub-01/ses-2mo/func/sub-01_ses-2mo_task-rest_space-MNIInfant+2_desc-preproc_bold.nii.gz"
+    ],
+    "SpatialReference": "https://templateflow.s3.amazonaws.com/tpl-MNIInfant_cohort-2_res-01_T1w.nii.gz",
+    "index_17network": {
+        "Description": "The corresponding integer value of this node in the 17-network Schaefer atlas imaging file.",
+        "LongName": "Node index from Schaefer 17-network atlas"
+    },
+    "name_17network": {
+        "Description": "The label of the node as it appears in the canonical Schaefer 17-network atlas.",
+        "LongName": "Node label from Schaefer 17-network atlas"
+    },
+    "name_7network": {
+        "Description": "The label of the node as it appears in the canonical Schaefer 7-network atlas.",
+        "LongName": "Node label from Schaefer 7-network atlas"
+    },
+    "network_label_17network": {
+        "Description": "The name of the network this node is assigned to in the Schaefer 17-network atlas.",
+        "LongName": "Network label from Schaefer 17-network atlas"
+    }
+}

atlas-4S/sub-01/ses-2mo/func/sub-01_ses-2mo_space-MNIInfant+2_atlas-4S_scale-256_dseg.json

@@ -0,0 +1,24 @@
+{
+    "Manual": "false",
+    "Sources": [
+        "bids::tpl-MNIInfant/cohort-2/anat/tpl-MNIInfant_cohort-2_atlas-4S_scale-256_res-01_dseg.nii.gz",
+        "bids::sub-01/ses-2mo/func/sub-01_ses-2mo_task-rest_space-MNIInfant+2_desc-preproc_bold.nii.gz"
+    ],
+    "SpatialReference": "https://templateflow.s3.amazonaws.com/tpl-MNIInfant_cohort-2_res-01_T1w.nii.gz",
+    "index_17network": {
+        "Description": "The corresponding integer value of this node in the 17-network Schaefer atlas imaging file.",
+        "LongName": "Node index from Schaefer 17-network atlas"
+    },
+    "name_17network": {
+        "Description": "The label of the node as it appears in the canonical Schaefer 17-network atlas.",
+        "LongName": "Node label from Schaefer 17-network atlas"
+    },
+    "name_7network": {
+        "Description": "The label of the node as it appears in the canonical Schaefer 7-network atlas.",
+        "LongName": "Node label from Schaefer 7-network atlas"
+    },
+    "network_label_17network": {
+        "Description": "The name of the network this node is assigned to in the Schaefer 17-network atlas.",
+        "LongName": "Network label from Schaefer 17-network atlas"
+    }
+}

atlas-4S/sub-01/ses-2mo/func/sub-01_ses-2mo_space-boldref_atlas-4S_scale-156_dseg.json

@@ -0,0 +1,24 @@
+{
+    "Manual": "false",
+    "Sources": [
+        "bids::tpl-MNIInfant/cohort-2/anat/tpl-MNIInfant_cohort-1_atlas-4S_scale-156_res-01_dseg.nii.gz",
+        "bids::sub-01/ses-2mo/func/sub-01_ses-2mo_task-rest_space-boldref_desc-preproc_bold.nii.gz"
+    ],
+    "SpatialReference": "bids::sub-01/ses-2mo/func/sub-01_ses-2mo_task-rest_space-boldref_desc-preproc_bold.nii.gz",
+    "index_17network": {
+        "Description": "The corresponding integer value of this node in the 17-network Schaefer atlas imaging file.",
+        "LongName": "Node index from Schaefer 17-network atlas"
+    },
+    "name_17network": {
+        "Description": "The label of the node as it appears in the canonical Schaefer 17-network atlas.",
+        "LongName": "Node label from Schaefer 17-network atlas"
+    },
+    "name_7network": {
+        "Description": "The label of the node as it appears in the canonical Schaefer 7-network atlas.",
+        "LongName": "Node label from Schaefer 7-network atlas"
+    },
+    "network_label_17network": {
+        "Description": "The name of the network this node is assigned to in the Schaefer 17-network atlas.",
+        "LongName": "Network label from Schaefer 17-network atlas"
+    }
+}

atlas-4S/sub-01/ses-2mo/func/sub-01_ses-2mo_space-boldref_atlas-4S_scale-256_dseg.json

@@ -0,0 +1,24 @@
+{
+    "Manual": "false",
+    "Sources": [
+        "bids::tpl-MNIInfant/cohort-2/anat/tpl-MNIInfant_cohort-1_atlas-4S_scale-256_res-01_dseg.nii.gz",
+        "bids::sub-01/ses-2mo/func/sub-01_ses-2mo_task-rest_space-boldref_desc-preproc_bold.nii.gz"
+    ],
+    "SpatialReference": "bids::sub-01/ses-2mo/func/sub-01_ses-2mo_task-rest_space-boldref_desc-preproc_bold.nii.gz",
+    "index_17network": {
+        "Description": "The corresponding integer value of this node in the 17-network Schaefer atlas imaging file.",
+        "LongName": "Node index from Schaefer 17-network atlas"
+    },
+    "name_17network": {
+        "Description": "The label of the node as it appears in the canonical Schaefer 17-network atlas.",
+        "LongName": "Node label from Schaefer 17-network atlas"
+    },
+    "name_7network": {
+        "Description": "The label of the node as it appears in the canonical Schaefer 7-network atlas.",
+        "LongName": "Node label from Schaefer 7-network atlas"
+    },
+    "network_label_17network": {
+        "Description": "The name of the network this node is assigned to in the Schaefer 17-network atlas.",
+        "LongName": "Network label from Schaefer 17-network atlas"
+    }
+}