Atlases used in C-PAC v1.8.7 rbc-options: ReproBrainChart-options preconfigured pipeline:
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: AvgThese atlases are collected here along with tabular files listing the ROI labels and metadata from the atlas' respective sources in the configuration (please see the original atlas' respective sources for individual licenses).
| source in configuration | filename |
|---|---|
/ndmg_atlases/label/Human/AAL_space-MNI152NLin6_res-2x2x2.nii.gz |
atlas-AAL_space-MNI152NLin6_res-2_dseg |
/ndmg_atlases/label/Human/Brodmann_space-MNI152NLin6_res-2x2x2.nii.gz |
atlas-Brodmann_space-MNI152NLin6_res-2_dseg |
/ndmg_atlases/label/Human/Glasser_space-MNI152NLin6_res-2x2x2.nii.gz |
atlas-Glasser_space-MNI152NLin6_res-2_dseg |
/ndmg_atlases/label/Human/Slab907_space-MNI152NLin6_res-2x2x2.nii.gz |
atlas-Slab907_space-MNI152NLin6_res-2_dseg |
/ndmg_atlases/label/Human/HarvardOxfordcort-maxprob-thr25_space-MNI152NLin6_res-2x2x2.nii.gz |
atlas-HarvardOxfordcortMaxprobThr25_space-MNI152NLin6_res-2_dseg |
/ndmg_atlases/label/Human/HarvardOxfordsub-maxprob-thr25_space-MNI152NLin6_res-2x2x2.nii.gz |
atlas-HarvardOxfordsubMaxprobThr25_space-MNI152NLin6_res-2_dseg |
/ndmg_atlases/label/Human/Juelich_space-MNI152NLin6_res-2x2x2.nii.gz |
atlas-Juelich_space-MNI152NLin6_res-2_dseg |
/cpac_templates/CC200.nii.gz |
atlas-CC200_space-MNI152NLin6_res-2_dseg |
/cpac_templates/CC400.nii.gz |
atlas-CC400_space-MNI152NLin6_res-2_dseg |
/cpac_templates/Schaefer2018_space-FSLMNI152_res-2mm_desc-200Parcels17NetworksOrder.nii.gz |
atlas-Schaefer2018_space-MNI152NLin6_res-2_desc-200Parcels17NetworksOrder_dseg |
/cpac_templates/Schaefer2018_space-FSLMNI152_res-2mm_desc-300Parcels17NetworksOrder.nii.gz |
atlas-Schaefer2018_space-MNI152NLin6_res-2_desc-300Parcels17NetworksOrder_dseg |
/cpac_templates/Schaefer2018_space-FSLMNI152_res-2mm_desc-400Parcels17NetworksOrder.nii.gz |
atlas-Schaefer2018_space-MNI152NLin6_res-2_desc-400Parcels17NetworksOrder_dseg |
/cpac_templates/Schaefer2018_space-FSLMNI152_res-2mm_desc-1000Parcels17NetworksOrder.nii.gz |
atlas-Schaefer2018_space-MNI152NLin6_res-2_desc-1000Parcels17NetworksOrder_dseg |
/ndmg_atlases/label/Human/Yeo-17-liberal_space-MNI152NLin6_res-2x2x2.nii.gz |
atlas-Yeo17liberal_space-MNI152NLin6_res-2_dseg |
/ndmg_atlases/label/Human/Yeo-17_space-MNI152NLin6_res-2x2x2.nii.gz |
atlas-Yeo17_space-MNI152NLin6_res-2_dseg |
/ndmg_atlases/label/Human/Yeo-7-liberal_space-MNI152NLin6_res-2x2x2.nii.gz |
atlas-Yeo7liberal_space-MNI152NLin6_res-2_dseg |
/ndmg_atlases/label/Human/Yeo-7_space-MNI152NLin6_res-2x2x2.nii.gz |
atlas-Yeo7_space-MNI152NLin6_res-2_dseg |
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:
| Key name | Requirement Level | Data type | Description |
|---|---|---|---|
| MetaData | REQUIRED | object | Atlas metadata, largely as defined in Neuroparc Contribution Criteria § File 2: Atlas Information with modifications noted here. |
| rois | REQUIRED | object | Parcellation regions metadata largely as defined in Neuroparc Contribution Criteria § File 2: Atlas Information with modifications noted here. |
| Key name | Requirement Level | Data type | Description |
|---|---|---|---|
| AtlasName | REQUIRED | string | This should be the same as in the filename. |
| Description | RECOMMENDED | string | Provide a use case for the atlas that someone looking through the list of atlases can understand. |
| Native Coordinate Space | RECOMMENDED | string | The coordinate space the atlas is defined in (i.e. Talairach or MNI). |
| Hierarchical | OPTIONAL | boolean | If the atlas consists of hierarchical components (meaning there are subregions), this value should be true and false if otherwise. |
| Symmetrical | OPTIONAL | boolean | If the atlas is designed to be symmetrical, this value should be true and false otherwise. |
| Number of Regions | OPTIONAL | integer string | The number of regions defined by the atlas, not including empty space. |
| Average Volume Per Region | OPTIONAL | float string | The average volume of all regions, not including empty space. |
| Year Generated | OPTIONAL | integer string | The year the atlas was first created, not the date of submission or the date of publication. |
| Generation Method | OPTIONAL | string | A brief (2-3 sentences) description of the method used to produce the atlas. |
| Source | RECOMMENDED | string | If the atlas has been published, please link the paper here if it is available. |
| Key name | Key type | Requirement Level | Data type | Description |
|---|---|---|---|---|
"0" |
literal string: "0" |
REQUIRED | object | Background region. |
| region | integer string | REQUIRED | object | Region of interest. |
| Key name | Requirement Level | Data type | Description |
|---|---|---|---|
| label | RECOMMENDED | literal string: "background" |
As shown in BEP038 draft. |
| center | REQUIRED | null | Must be null for empty space. |
| Key name | Requirement Level | Data type | Description |
|---|---|---|---|
| label | REQUIRED | string | Provide a common name for the region. Numerical values are acceptable if the atlas is generative. |
| center | REQUIRED | numeric string | 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 | Size must be specified in voxels according to the resolution in the file name. |