From 5191351814e56d74bb04d5b0f739445dc80e7065 Mon Sep 17 00:00:00 2001 From: Jon Clucas Date: Mon, 17 Jun 2024 14:23:02 -0400 Subject: [PATCH] :memo: Collect metadata from sources --- sourcedata/atlases/README.md | 75 +++++++++++++++++++ ...tlas-AAL_space-MNI152NLin6_res-2_dseg.json | 11 ++- ...Brodmann_space-MNI152NLin6_res-2_dseg.json | 11 ++- ...as-CC200_space-MNI152NLin6_res-2_dseg.json | 5 -- ...as-CC400_space-MNI152NLin6_res-2_dseg.json | 5 -- ...-Glasser_space-MNI152NLin6_res-2_dseg.json | 11 ++- ...robThr25_space-MNI152NLin6_res-2_dseg.json | 11 ++- ...robThr25_space-MNI152NLin6_res-2_dseg.json | 11 ++- ...-Juelich_space-MNI152NLin6_res-2_dseg.json | 10 +-- ..._desc-1000Parcels17NetworksOrder_dseg.json | 6 +- ...2_desc-200Parcels17NetworksOrder_dseg.json | 6 +- ...2_desc-300Parcels17NetworksOrder_dseg.json | 6 +- ...2_desc-400Parcels17NetworksOrder_dseg.json | 6 +- ...-Slab907_space-MNI152NLin6_res-2_dseg.json | 8 +- ...as-Yeo17_space-MNI152NLin6_res-2_dseg.json | 11 ++- ...7liberal_space-MNI152NLin6_res-2_dseg.json | 11 ++- ...las-Yeo7_space-MNI152NLin6_res-2_dseg.json | 11 ++- ...7liberal_space-MNI152NLin6_res-2_dseg.json | 11 ++- sourcedata/atlases/dataset_description.json | 42 +++++++++++ 19 files changed, 173 insertions(+), 95 deletions(-) create mode 100644 sourcedata/atlases/README.md create mode 100644 sourcedata/atlases/dataset_description.json diff --git a/sourcedata/atlases/README.md b/sourcedata/atlases/README.md new file mode 100644 index 0000000..828421a --- /dev/null +++ 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 ROI 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 index f51b7cb..c9fd253 100644 --- 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 index 7734204..ac00be2 100644 --- 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 index c8b2193..98d4b58 100644 --- 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 index 7b60c5f..9c03c25 100644 --- 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 index e40d86b..f2613dc 100644 --- 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 index bbbb305..78c4d62 100644 --- 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 index ef25bc2..01004d2 100644 --- 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 index 98904f1..3f1fb19 100644 --- 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/sourcedata/atlases/atlas-Schaefer2018_space-MNI152NLin6_res-2_desc-1000Parcels17NetworksOrder_dseg.json b/sourcedata/atlases/atlas-Schaefer2018_space-MNI152NLin6_res-2_desc-1000Parcels17NetworksOrder_dseg.json index 8ae3107..826be50 100644 --- a/sourcedata/atlases/atlas-Schaefer2018_space-MNI152NLin6_res-2_desc-1000Parcels17NetworksOrder_dseg.json +++ b/sourcedata/atlases/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/sourcedata/atlases/atlas-Schaefer2018_space-MNI152NLin6_res-2_desc-200Parcels17NetworksOrder_dseg.json b/sourcedata/atlases/atlas-Schaefer2018_space-MNI152NLin6_res-2_desc-200Parcels17NetworksOrder_dseg.json index 0c5b155..c68dc28 100644 --- a/sourcedata/atlases/atlas-Schaefer2018_space-MNI152NLin6_res-2_desc-200Parcels17NetworksOrder_dseg.json +++ b/sourcedata/atlases/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/sourcedata/atlases/atlas-Schaefer2018_space-MNI152NLin6_res-2_desc-300Parcels17NetworksOrder_dseg.json b/sourcedata/atlases/atlas-Schaefer2018_space-MNI152NLin6_res-2_desc-300Parcels17NetworksOrder_dseg.json index 07c6ab3..d20d866 100644 --- a/sourcedata/atlases/atlas-Schaefer2018_space-MNI152NLin6_res-2_desc-300Parcels17NetworksOrder_dseg.json +++ b/sourcedata/atlases/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/sourcedata/atlases/atlas-Schaefer2018_space-MNI152NLin6_res-2_desc-400Parcels17NetworksOrder_dseg.json b/sourcedata/atlases/atlas-Schaefer2018_space-MNI152NLin6_res-2_desc-400Parcels17NetworksOrder_dseg.json index 055fe45..45fa9f8 100644 --- a/sourcedata/atlases/atlas-Schaefer2018_space-MNI152NLin6_res-2_desc-400Parcels17NetworksOrder_dseg.json +++ b/sourcedata/atlases/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 index ff647e6..cbce24f 100644 --- 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 index dec913c..51a5e78 100644 --- 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 index dc1f6f3..96d0e26 100644 --- 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 index 9014453..a4fe83a 100644 --- 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 index 76aaf41..2451ae2 100644 --- 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": { diff --git a/sourcedata/atlases/dataset_description.json b/sourcedata/atlases/dataset_description.json new file mode 100644 index 0000000..76b3334 --- /dev/null +++ b/sourcedata/atlases/dataset_description.json @@ -0,0 +1,42 @@ +{ + "Name": "Atlases for https://fcp-indi.github.io/docs/v1.8.7/user/pipelines/preconfig#rbc-options-reprobrainchart-options-pipeline", + "BIDSVersion": "1.9.0", + "DatasetType": "derivative", + "License": "CC0", + "Authors": [ + "Jon Clucas", + "Matt Cieslak" + ], + "GeneratedBy": [ + { + "Name": "Manual", + "Description": "Collected from C-PAC sources and reformatted toward BEP038 draft https://docs.google.com/document/d/e/2PACX-1vQ39OGa0-r_8bxpmKsajfgbQsLLUAE6RrXU7bA2I_IOJfhvn7GWRp6u5-Ys2vnVcJA3JQfHbojDdvVo/pub" + } + ], + "SourceDatasets": [ + { + "URL": "https://github.com/FCP-INDI/C-PAC/blob/v1.8.7/CPAC/resources/configs/pipeline_config_rbc-options.yml", + "Version": "v1.8.7" + }, + { + "URL": "https://github.com/FCP-INDI/C-PAC_templates/tree/v1.8.6-2", + "Version": "v1.8.6-2" + }, + { + "URL": "https://github.com/neurodata/neuroparc/tree/v1.0", + "Version": "v1.0" + }, + { + "URL": "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", + "Version": "v0.22.6-Edit_KRR_LITE_to_only_allow_for_corr_kernel" + }, + { + "URL": "https://ccraddock.github.io/cluster_roi/", + "Version": "v1.0.0" + }, + { + "URL": "https://docs.google.com/document/d/1RxW4cARr3-EiBEcXjLpSIVidvnUSHE7yJCUY91i5TfM", + "Version": "https://docs.google.com/document/d/e/2PACX-1vQ39OGa0-r_8bxpmKsajfgbQsLLUAE6RrXU7bA2I_IOJfhvn7GWRp6u5-Ys2vnVcJA3JQfHbojDdvVo/pub" + } + ] +} \ No newline at end of file