📝 Collect metadata from sources

FCP-INDI · Jun 17, 2024 · 5191351 · 5191351
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diff --git a/sourcedata/atlases/README.md b/sourcedata/atlases/README.md
@@ -0,0 +1,75 @@
+# Atlases for `rbc-options` preconfigured C-PAC pipeline
+
+Atlases used in [C-PAC v1.8.7 `rbc-options`: ReproBrainChart-options preconfigured pipeline](https://fcp-indi.github.io/docs/v1.8.7/user/pipelines/preconfig#rbc-options-reprobrainchart-options-pipeline):
+
+```YAML
+timeseries_extraction:
+  tse_roi_paths:
+    /ndmg_atlases/label/Human/AAL_space-MNI152NLin6_res-2x2x2.nii.gz: Avg
+    /ndmg_atlases/label/Human/Brodmann_space-MNI152NLin6_res-2x2x2.nii.gz: Avg
+    /ndmg_atlases/label/Human/Glasser_space-MNI152NLin6_res-2x2x2.nii.gz: Avg
+    /ndmg_atlases/label/Human/Slab907_space-MNI152NLin6_res-2x2x2.nii.gz: Avg
+    /ndmg_atlases/label/Human/HarvardOxfordcort-maxprob-thr25_space-MNI152NLin6_res-2x2x2.nii.gz: Avg
+    /ndmg_atlases/label/Human/HarvardOxfordsub-maxprob-thr25_space-MNI152NLin6_res-2x2x2.nii.gz: Avg
+    /ndmg_atlases/label/Human/Juelich_space-MNI152NLin6_res-2x2x2.nii.gz: Avg
+    /cpac_templates/CC200.nii.gz: Avg
+    /cpac_templates/CC400.nii.gz: Avg
+    /cpac_templates/Schaefer2018_space-FSLMNI152_res-2mm_desc-200Parcels17NetworksOrder.nii.gz: Avg
+    /cpac_templates/Schaefer2018_space-FSLMNI152_res-2mm_desc-300Parcels17NetworksOrder.nii.gz: Avg
+    /cpac_templates/Schaefer2018_space-FSLMNI152_res-2mm_desc-400Parcels17NetworksOrder.nii.gz: Avg
+    /cpac_templates/Schaefer2018_space-FSLMNI152_res-2mm_desc-1000Parcels17NetworksOrder.nii.gz: Avg
+    /ndmg_atlases/label/Human/Yeo-17-liberal_space-MNI152NLin6_res-2x2x2.nii.gz: Avg
+    /ndmg_atlases/label/Human/Yeo-17_space-MNI152NLin6_res-2x2x2.nii.gz: Avg
+    /ndmg_atlases/label/Human/Yeo-7-liberal_space-MNI152NLin6_res-2x2x2.nii.gz: Avg
+    /ndmg_atlases/label/Human/Yeo-7_space-MNI152NLin6_res-2x2x2.nii.gz: Avg
+```
+
+These atlases are collected here along with [tabular files](https://bids-specification.readthedocs.io/en/stable/common-principles.html#tabular-files) listing the <span title="region of interest">ROI</span> labels and metadata from the atlas' respective sources.
+
+The filenames here correspond to the BIDS-style strings the atlases are referenced as in C-PAC's outputs rather than corresponding to the filenames in the configuration definition.
+
+The metadata are formatted as described below:
+
+## Atlas JSON metadata
+
+| Key name | Requirement Level | Data type | Description |
+| --- | --- | --- | --- |
+| [MetaData](#metadata) | REQUIRED | [object](https://www.json.org/json-en.html) | Atlas metadata, largely as defined in [Neuroparc Contribution Criteria § File 2: Atlas Information](https://github.com/neurodata/neuroparc/blob/master/CONTRIBUTING.md#file-2-atlas-information) with modifications noted here. |
+| [rois](#rois) | REQUIRED | [object](https://www.json.org/json-en.html) | Parcellation regions metadata largely as defined in [Neuroparc Contribution Criteria § File 2: Atlas Information](https://github.com/neurodata/neuroparc/blob/master/CONTRIBUTING.md#file-2-atlas-information) with modifications noted here. |
+
+### Metadata
+
+| Key name | Requirement Level | Data type | Description |
+| --- | --- | --- | --- |
+| AtlasName | REQUIRED | [string](https://www.w3schools.com/js/js_json_datatypes.asp) | This should be the same as in the filename. |
+| Description | RECOMMENDED | [string](https://www.w3schools.com/js/js_json_datatypes.asp) | Provide a use case for the atlas that someone looking through the list of atlases can understand |
+| Native Coordinate Space | RECOMMENDED | [string](https://www.w3schools.com/js/js_json_datatypes.asp) | The coordinate space the atlas is defined in (i.e. Talairach or MNI). |
+| Hierarchical | OPTIONAL | [boolean](https://www.w3schools.com/js/js_json_datatypes.asp) | If the atlas consists of hierarchical components (meaning there are subregions), this value should be `true` and `false` if otherwise. |
+| Symmetrical | OPTIONAL | [boolean](https://www.w3schools.com/js/js_json_datatypes.asp) | If the atlas is designed to be symmetrical, this value should be `true` and `false` otherwise. |
+| Number of Regions | OPTIONAL | integer [string](https://www.w3schools.com/js/js_json_datatypes.asp) | The number of regions defined by the atlas, not including empty space. |
+| Average Volume Per Region | OPTIONAL | float [string](https://www.w3schools.com/js/js_json_datatypes.asp) | The average volume of all regions, not including empty space. |
+| Year Generated | OPTIONAL | integer [string](https://www.w3schools.com/js/js_json_datatypes.asp) | The year the atlas was first created, not the date of submission or the date of publication. |
+| Generation Method | OPTIONAL | [string](https://www.w3schools.com/js/js_json_datatypes.asp) | A brief (2-3 sentences) description of the method used to produce the atlas. |
+| Source | RECOMMENDED | [string](https://www.w3schools.com/js/js_json_datatypes.asp) | If the atlas has been published, please link the paper here if it is available. |
+
+### rois
+
+| Key name | Key type | Requirement Level | Data type | Description |
+| --- | --- | --- | --- | --- |
+| 0 | literal [string](https://www.w3schools.com/js/js_json_datatypes.asp): `"0"` |  REQUIRED | [object](https://www.json.org/json-en.html) | [Background region](#0). |
+| [region](#region) | integer [string](https://www.w3schools.com/js/js_json_datatypes.asp) | REQUIRED | [object](https://www.json.org/json-en.html) | [Region of interest](#region). |
+
+#### 0
+
+| Key name | Requirement Level | Data type | Description |
+| --- | --- | --- | --- |
+| label | RECOMMENDED | literal [string](https://www.w3schools.com/js/js_json_datatypes.asp): `"background"` | As shown in [BEP038 draft](https://docs.google.com/document/d/e/2PACX-1vQ39OGa0-r_8bxpmKsajfgbQsLLUAE6RrXU7bA2I_IOJfhvn7GWRp6u5-Ys2vnVcJA3JQfHbojDdvVo/pub). |
+| center | REQUIRED | [null](https://www.w3schools.com/js/js_json_datatypes.asp) | Must be `null` for empty space. |
+
+#### region
+
+| Key name | Requirement Level | Data type | Description |
+| --- | --- | --- | --- |
+| label | REQUIRED | [string](https://www.w3schools.com/js/js_json_datatypes.asp) | Provide a common name for the region. Numerical values are acceptable if the atlas is generative. |
+| center | REQUIRED | numeric [string](https://www.w3schools.com/js/js_json_datatypes.asp) | The center of the region should be defined relative to the coordinate system the atlas is in and the resolution of the atlas. |
+| size | REQUIRED | numeric [string](https://www.w3schools.com/js/js_json_datatypes.asp) | Size must be specified in voxels according to the resolution in the file name. |
diff --git a/sourcedata/atlases/atlas-AAL_space-MNI152NLin6_res-2_dseg.json b/sourcedata/atlases/atlas-AAL_space-MNI152NLin6_res-2_dseg.json
@@ -1,14 +1,13 @@
 {
     "MetaData": {
         "AtlasName": "AAL",
-        "Description": "",
-        "Native Coordinate Space": "",
-        "Hierarchical": "yes",
-        "Symmetrical": "no",
+        "Description": "Automated anatomical labelling based on sulci.",
+        "Hierarchical": true,
+        "Symmetrical": false,
         "Number of Regions": "116",
         "Average Volume Per Region": "1598.3189655172414",
-        "Year Generated": "2020",
-        "Generation Method": "",
+        "Year Generated": "2002",
+        "Generation Method": "Delineated with respect to anatomical landmarks (following sulci course in brain)",
         "Source": "https://www.ncbi.nlm.nih.gov/pubmed/11771995"
     },
     "rois": {

diff --git a/sourcedata/atlases/atlas-Brodmann_space-MNI152NLin6_res-2_dseg.json b/sourcedata/atlases/atlas-Brodmann_space-MNI152NLin6_res-2_dseg.json
@@ -1,14 +1,13 @@
 {
     "MetaData": {
         "AtlasName": "Brodmann",
-        "Description": "",
-        "Native Coordinate Space": "",
-        "Hierarchical": "no",
-        "Symmetrical": "yes",
+        "Description": "Brodman areas separated by gyri.",
+        "Hierarchical": false,
+        "Symmetrical": true,
         "Number of Regions": "41",
         "Average Volume Per Region": "4122.317073170731",
-        "Year Generated": "2020",
-        "Generation Method": "",
+        "Year Generated": "1909",
+        "Generation Method": "Corticall parcellation separating regions based on cellular morphology and organization",
         "Source": "https://scalablebrainatlas.incf.org/human/B05_on_Conte69"
     },
     "rois": {

diff --git a/sourcedata/atlases/atlas-CC200_space-MNI152NLin6_res-2_dseg.json b/sourcedata/atlases/atlas-CC200_space-MNI152NLin6_res-2_dseg.json
@@ -1,14 +1,9 @@
 {
     "MetaData": {
         "AtlasName": "CC200",
-        "Description": "",
-        "Native Coordinate Space": "",
-        "Hierarchical": "",
-        "Symmetrical": "",
         "Number of Regions": "200",
         "Average Volume Per Region": "217.065",
         "Year Generated": "2011",
-        "Generation Method": "",
         "Source": "https://ccraddock.github.io/cluster_roi/atlases.html"
     },
     "rois": {

diff --git a/sourcedata/atlases/atlas-CC400_space-MNI152NLin6_res-2_dseg.json b/sourcedata/atlases/atlas-CC400_space-MNI152NLin6_res-2_dseg.json
@@ -1,14 +1,9 @@
 {
     "MetaData": {
         "AtlasName": "CC400",
-        "Description": "",
-        "Native Coordinate Space": "",
-        "Hierarchical": "",
-        "Symmetrical": "",
         "Number of Regions": "392",
         "Average Volume Per Region": "110.74744897959184",
         "Year Generated": "2011",
-        "Generation Method": "",
         "Source": "https://ccraddock.github.io/cluster_roi/atlases.html"
     },
     "rois": {

diff --git a/sourcedata/atlases/atlas-Glasser_space-MNI152NLin6_res-2_dseg.json b/sourcedata/atlases/atlas-Glasser_space-MNI152NLin6_res-2_dseg.json
@@ -1,14 +1,13 @@
 {
     "MetaData": {
         "AtlasName": "Glasser",
-        "Description": "",
-        "Native Coordinate Space": "",
-        "Hierarchical": "no",
-        "Symmetrical": "yes",
+        "Description": "Cortical parcellation from multi-modal images of 210 adults in HCP.",
+        "Hierarchical": false,
+        "Symmetrical": true,
         "Number of Regions": "180",
         "Average Volume Per Region": "521.9944444444444",
-        "Year Generated": "2020",
-        "Generation Method": "",
+        "Year Generated": "2016",
+        "Generation Method": "Semi-automated. Separated based on function, connectivity, cortical architecture, topography, and expert analysis.",
         "Source": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4990127/"
     },
     "rois": {

diff --git a/sourcedata/atlases/atlas-HarvardOxfordcortMaxprobThr25_space-MNI152NLin6_res-2_dseg.json b/sourcedata/atlases/atlas-HarvardOxfordcortMaxprobThr25_space-MNI152NLin6_res-2_dseg.json
@@ -1,14 +1,13 @@
 {
     "MetaData": {
         "AtlasName": "HarvardOxford Cortical",
-        "Description": "",
-        "Native Coordinate Space": "",
-        "Hierarchical": "no",
-        "Symmetrical": "yes",
+        "Description": "Neuroanatomic subdivisions delineated by this general segmentation generaly corresponding to natural gray matter boundaries.",
+        "Hierarchical": false,
+        "Symmetrical": true,
         "Number of Regions": "48",
         "Average Volume Per Region": "2744.1458333333335",
-        "Year Generated": "2020",
-        "Generation Method": "",
+        "Year Generated": "2005",
+        "Generation Method": "Created by subdividing neocortex by topographic criteria into 48 parcellation units corresponding to the principal cerebral gyri.",
         "Source": "https://scalablebrainatlas.incf.org/human/HOA06"
     },
     "rois": {

diff --git a/sourcedata/atlases/atlas-HarvardOxfordsubMaxprobThr25_space-MNI152NLin6_res-2_dseg.json b/sourcedata/atlases/atlas-HarvardOxfordsubMaxprobThr25_space-MNI152NLin6_res-2_dseg.json
@@ -1,14 +1,13 @@
 {
     "MetaData": {
         "AtlasName": "HarvardOxford Subcortical",
-        "Description": "",
-        "Native Coordinate Space": "",
-        "Hierarchical": "no",
-        "Symmetrical": "no",
+        "Description": "Neuroanatomic subdivisions delineated by this general segmentation generaly corresponding to natural gray matter boundaries.",
+        "Hierarchical": false,
+        "Symmetrical": false,
         "Number of Regions": "21",
         "Average Volume Per Region": "9764.380952380952",
-        "Year Generated": "2020",
-        "Generation Method": "",
+        "Year Generated": "2005",
+        "Generation Method": "Created by subdividing neocortex by topographic criteria into 48 parcellation units corresponding to the principal cerebral gyri.",
         "Source": "https://scalablebrainatlas.incf.org/human/HOA06"
     },
     "rois": {

diff --git a/sourcedata/atlases/atlas-Juelich_space-MNI152NLin6_res-2_dseg.json b/sourcedata/atlases/atlas-Juelich_space-MNI152NLin6_res-2_dseg.json
@@ -1,14 +1,12 @@
 {
     "MetaData": {
         "AtlasName": "Juelich",
-        "Description": "",
-        "Native Coordinate Space": "",
-        "Hierarchical": "yes",
-        "Symmetrical": "no",
+        "Hierarchical": true,
+        "Symmetrical": false,
         "Number of Regions": "103",
         "Average Volume Per Region": "616.9902912621359",
-        "Year Generated": "2020",
-        "Generation Method": "",
+        "Year Generated": "2005",
+        "Generation Method": "Probabilistic atlas created by averaging multi-subject post-mortem cyto- and myelo-architectonic segmentations.",
         "Source": "https://scalablebrainatlas.incf.org/human/EAZ05_v18"
     },
     "rois": {

diff --git a/...ases/atlas-Schaefer2018_space-MNI152NLin6_res-2_desc-1000Parcels17NetworksOrder_dseg.json b/...ases/atlas-Schaefer2018_space-MNI152NLin6_res-2_desc-1000Parcels17NetworksOrder_dseg.json
@@ -1,14 +1,10 @@
 {
     "MetaData": {
         "AtlasName": "Schaefer2018_1000Parcels17NetworksOrder",
-        "Description": "",
-        "Native Coordinate Space": "",
-        "Hierarchical": "",
-        "Symmetrical": "",
         "Number of Regions": "1000",
         "Average Volume Per Region": "132.032",
         "Year Generated": "2018",
-        "Generation Method": "",
+        "Generation Method": "Resting state fMRI data from 1489 subjects were registered using surface-based alignment. A gradient weighted markov random field approach was employed to identify cortical parcels ranging from 100 to 1000 parcels.",
         "Source": "https://github.com/ThomasYeoLab/CBIG/tree/v0.22.6-Edit_KRR_LITE_to_only_allow_for_corr_kernel/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal/Parcellations/MNI"
     },
     "rois": {

diff --git a/...lases/atlas-Schaefer2018_space-MNI152NLin6_res-2_desc-200Parcels17NetworksOrder_dseg.json b/...lases/atlas-Schaefer2018_space-MNI152NLin6_res-2_desc-200Parcels17NetworksOrder_dseg.json
@@ -1,14 +1,10 @@
 {
     "MetaData": {
         "AtlasName": "Schaefer2018_200Parcels17NetworksOrder",
-        "Description": "",
-        "Native Coordinate Space": "",
-        "Hierarchical": "",
-        "Symmetrical": "",
         "Number of Regions": "200",
         "Average Volume Per Region": "660.16",
         "Year Generated": "2018",
-        "Generation Method": "",
+        "Generation Method": "Resting state fMRI data from 1489 subjects were registered using surface-based alignment. A gradient weighted markov random field approach was employed to identify cortical parcels ranging from 100 to 1000 parcels.",
         "Source": "https://github.com/ThomasYeoLab/CBIG/tree/v0.22.6-Edit_KRR_LITE_to_only_allow_for_corr_kernel/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal/Parcellations/MNI"
     },
     "rois": {

diff --git a/...lases/atlas-Schaefer2018_space-MNI152NLin6_res-2_desc-300Parcels17NetworksOrder_dseg.json b/...lases/atlas-Schaefer2018_space-MNI152NLin6_res-2_desc-300Parcels17NetworksOrder_dseg.json
@@ -1,14 +1,10 @@
 {
     "MetaData": {
         "AtlasName": "Schaefer2018_300Parcels17NetworksOrder",
-        "Description": "",
-        "Native Coordinate Space": "",
-        "Hierarchical": "",
-        "Symmetrical": "",
         "Number of Regions": "134",
         "Average Volume Per Region": "372.46268656716416",
         "Year Generated": "2018",
-        "Generation Method": "",
+        "Generation Method": "Resting state fMRI data from 1489 subjects were registered using surface-based alignment. A gradient weighted markov random field approach was employed to identify cortical parcels ranging from 100 to 1000 parcels.",
         "Source": "https://github.com/ThomasYeoLab/CBIG/tree/v0.22.6-Edit_KRR_LITE_to_only_allow_for_corr_kernel/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal/Parcellations/MNI"
     },
     "rois": {

diff --git a/...lases/atlas-Schaefer2018_space-MNI152NLin6_res-2_desc-400Parcels17NetworksOrder_dseg.json b/...lases/atlas-Schaefer2018_space-MNI152NLin6_res-2_desc-400Parcels17NetworksOrder_dseg.json
@@ -1,14 +1,10 @@
 {
     "MetaData": {
         "AtlasName": "Schaefer2018_400Parcels17NetworksOrder",
-        "Description": "",
-        "Native Coordinate Space": "",
-        "Hierarchical": "",
-        "Symmetrical": "",
         "Number of Regions": "400",
         "Average Volume Per Region": "330.08",
         "Year Generated": "2018",
-        "Generation Method": "",
+        "Generation Method": "Resting state fMRI data from 1489 subjects were registered using surface-based alignment. A gradient weighted markov random field approach was employed to identify cortical parcels ranging from 100 to 1000 parcels.",
         "Source": "https://github.com/ThomasYeoLab/CBIG/tree/v0.22.6-Edit_KRR_LITE_to_only_allow_for_corr_kernel/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal/Parcellations/MNI"
     },
     "rois": {

diff --git a/sourcedata/atlases/atlas-Slab907_space-MNI152NLin6_res-2_dseg.json b/sourcedata/atlases/atlas-Slab907_space-MNI152NLin6_res-2_dseg.json
@@ -1,14 +1,12 @@
 {
     "MetaData": {
         "AtlasName": "Slab907",
-        "Description": "",
-        "Native Coordinate Space": "",
-        "Hierarchical": "",
-        "Symmetrical": "no",
+        "Description": "Grid of ROI points spanning entire MNI brain volume.",
+        "Symmetrical": false,
         "Number of Regions": "907",
         "Average Volume Per Region": "54.02866593164278",
         "Year Generated": "2014",
-        "Generation Method": "",
+        "Generation Method": "Placed 907 ROIs at regular intervals throughout the cortex.",
         "Source": "https://doi.org/10.1073/pnas.1407787111"
     },
     "rois": {

diff --git a/sourcedata/atlases/atlas-Yeo17_space-MNI152NLin6_res-2_dseg.json b/sourcedata/atlases/atlas-Yeo17_space-MNI152NLin6_res-2_dseg.json
@@ -1,14 +1,13 @@
 {
     "MetaData": {
         "AtlasName": "Yeo-17",
-        "Description": "",
-        "Native Coordinate Space": "",
-        "Hierarchical": "no",
-        "Symmetrical": "yes",
+        "Description": "Local networks confined to sensory and motor cortices, functional connectivity followed topographic representations across adjacent areas.",
+        "Hierarchical": false,
+        "Symmetrical": true,
         "Number of Regions": "17",
         "Average Volume Per Region": "3881.4117647058824",
-        "Year Generated": "2020",
-        "Generation Method": "",
+        "Year Generated": "2011",
+        "Generation Method": "Clustered to identify networks of functionally coupled regions.",
         "Source": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3174820/"
     },
     "rois": {

diff --git a/sourcedata/atlases/atlas-Yeo17liberal_space-MNI152NLin6_res-2_dseg.json b/sourcedata/atlases/atlas-Yeo17liberal_space-MNI152NLin6_res-2_dseg.json
@@ -1,14 +1,13 @@
 {
     "MetaData": {
         "AtlasName": "Yeo-17 liberal",
-        "Description": "",
-        "Native Coordinate Space": "",
-        "Hierarchical": "no",
-        "Symmetrical": "yes",
+        "Description": "Local networks confined to sensory and motor cortices, functional connectivity followed topographic representations across adjacent areas.",
+        "Hierarchical": false,
+        "Symmetrical": true,
         "Number of Regions": "17",
         "Average Volume Per Region": "7759.882352941177",
-        "Year Generated": "2020",
-        "Generation Method": "",
+        "Year Generated": "2011",
+        "Generation Method": "Clustered to identify networks of functionally coupled regions.",
         "Source": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3174820/"
     },
     "rois": {

diff --git a/sourcedata/atlases/atlas-Yeo7_space-MNI152NLin6_res-2_dseg.json b/sourcedata/atlases/atlas-Yeo7_space-MNI152NLin6_res-2_dseg.json
@@ -1,14 +1,13 @@
 {
     "MetaData": {
         "AtlasName": "Yeo-7",
-        "Description": "",
-        "Native Coordinate Space": "",
-        "Hierarchical": "no",
-        "Symmetrical": "yes",
+        "Description": "Local networks confined to sensory and motor cortices, functional connectivity followed topographic representations across adjacent areas.",
+        "Hierarchical": false,
+        "Symmetrical": true,
         "Number of Regions": "7",
         "Average Volume Per Region": "9426.285714285714",
-        "Year Generated": "2020",
-        "Generation Method": "",
+        "Year Generated": "2011",
+        "Generation Method": "Clustered to identify networks of functionally coupled regions.",
         "Source": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3174820/"
     },
     "rois": {

diff --git a/sourcedata/atlases/atlas-Yeo7liberal_space-MNI152NLin6_res-2_dseg.json b/sourcedata/atlases/atlas-Yeo7liberal_space-MNI152NLin6_res-2_dseg.json
@@ -1,14 +1,13 @@
 {
     "MetaData": {
         "AtlasName": "Yeo-7 liberal",
-        "Description": "",
-        "Native Coordinate Space": "",
-        "Hierarchical": "no",
-        "Symmetrical": "yes",
+        "Description": "Local networks confined to sensory and motor cortices, functional connectivity followed topographic representations across adjacent areas.",
+        "Hierarchical": false,
+        "Symmetrical": true,
         "Number of Regions": "7",
         "Average Volume Per Region": "18845.428571428572",
-        "Year Generated": "2020",
-        "Generation Method": "",
+        "Year Generated": "2011",
+        "Generation Method": "Clustered to identify networks of functionally coupled regions.",
         "Source": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3174820/"
     },
     "rois": {