├── .circleci └── config.yml ├── .datalad ├── .gitattributes └── config ├── .gitattributes ├── .gitignore ├── 01_combine_subcortical.sh ├── 02_supplement_schaefers.sh ├── CIT168 ├── prepare_atlas.sh └── split_up_cit168.py ├── JointAtlas.html ├── JointAtlas.ipynb ├── README.md ├── Schaefer ├── 01_prepare_cifti_atlas.py ├── 02_generate_subcortical_cifti.sh ├── Atlas_ROIs.2.nii.gz ├── atlas-Schaefer2018v0143_desc-1000ParcelsAllNetworks_dseg.tsv ├── atlas-Schaefer2018v0143_desc-100ParcelsAllNetworks_dseg.tsv ├── atlas-Schaefer2018v0143_desc-200ParcelsAllNetworks_dseg.tsv ├── atlas-Schaefer2018v0143_desc-300ParcelsAllNetworks_dseg.tsv ├── atlas-Schaefer2018v0143_desc-400ParcelsAllNetworks_dseg.tsv ├── atlas-Schaefer2018v0143_desc-500ParcelsAllNetworks_dseg.tsv ├── atlas-Schaefer2018v0143_desc-600ParcelsAllNetworks_dseg.tsv ├── atlas-Schaefer2018v0143_desc-700ParcelsAllNetworks_dseg.tsv ├── atlas-Schaefer2018v0143_desc-800ParcelsAllNetworks_dseg.tsv ├── atlas-Schaefer2018v0143_desc-900ParcelsAllNetworks_dseg.tsv ├── prepare_atlas.sh ├── run_docker.sh ├── schaefer_ordering_mapper.py ├── test.sh ├── tpl-MNI152NLin2009cAsym_atlas-Schaefer2018v0143_res-01_desc-1000ParcelsAllNetworks_dseg.nii.gz ├── tpl-MNI152NLin2009cAsym_atlas-Schaefer2018v0143_res-01_desc-100ParcelsAllNetworks_dseg.nii.gz ├── tpl-MNI152NLin2009cAsym_atlas-Schaefer2018v0143_res-01_desc-200ParcelsAllNetworks_dseg.nii.gz ├── tpl-MNI152NLin2009cAsym_atlas-Schaefer2018v0143_res-01_desc-300ParcelsAllNetworks_dseg.nii.gz ├── tpl-MNI152NLin2009cAsym_atlas-Schaefer2018v0143_res-01_desc-400ParcelsAllNetworks_dseg.nii.gz ├── tpl-MNI152NLin2009cAsym_atlas-Schaefer2018v0143_res-01_desc-500ParcelsAllNetworks_dseg.nii.gz ├── tpl-MNI152NLin2009cAsym_atlas-Schaefer2018v0143_res-01_desc-600ParcelsAllNetworks_dseg.nii.gz ├── tpl-MNI152NLin2009cAsym_atlas-Schaefer2018v0143_res-01_desc-700ParcelsAllNetworks_dseg.nii.gz ├── tpl-MNI152NLin2009cAsym_atlas-Schaefer2018v0143_res-01_desc-800ParcelsAllNetworks_dseg.nii.gz ├── tpl-MNI152NLin2009cAsym_atlas-Schaefer2018v0143_res-01_desc-900ParcelsAllNetworks_dseg.nii.gz ├── tpl-MNI152NLin6Asym_atlas-Schaefer2018v0143_res-01_desc-1000ParcelsAllNetworks_dseg.nii.gz ├── tpl-MNI152NLin6Asym_atlas-Schaefer2018v0143_res-01_desc-100ParcelsAllNetworks_dseg.nii.gz ├── tpl-MNI152NLin6Asym_atlas-Schaefer2018v0143_res-01_desc-200ParcelsAllNetworks_dseg.nii.gz ├── tpl-MNI152NLin6Asym_atlas-Schaefer2018v0143_res-01_desc-300ParcelsAllNetworks_dseg.nii.gz ├── tpl-MNI152NLin6Asym_atlas-Schaefer2018v0143_res-01_desc-400ParcelsAllNetworks_dseg.nii.gz ├── tpl-MNI152NLin6Asym_atlas-Schaefer2018v0143_res-01_desc-500ParcelsAllNetworks_dseg.nii.gz ├── tpl-MNI152NLin6Asym_atlas-Schaefer2018v0143_res-01_desc-600ParcelsAllNetworks_dseg.nii.gz ├── tpl-MNI152NLin6Asym_atlas-Schaefer2018v0143_res-01_desc-700ParcelsAllNetworks_dseg.nii.gz ├── tpl-MNI152NLin6Asym_atlas-Schaefer2018v0143_res-01_desc-800ParcelsAllNetworks_dseg.nii.gz ├── tpl-MNI152NLin6Asym_atlas-Schaefer2018v0143_res-01_desc-900ParcelsAllNetworks_dseg.nii.gz ├── tpl-MNI152NLin6Asym_atlas-SubcorticalMerged_res-02_desc-Schaefer2018v0143x1000ParcelsLabels_dseg.nii.gz ├── tpl-MNI152NLin6Asym_atlas-SubcorticalMerged_res-02_desc-Schaefer2018v0143x1000Parcels_dseg.nii.gz ├── tpl-MNI152NLin6Asym_atlas-SubcorticalMerged_res-02_desc-Schaefer2018v0143x100ParcelsLabels_dseg.nii.gz ├── tpl-MNI152NLin6Asym_atlas-SubcorticalMerged_res-02_desc-Schaefer2018v0143x100Parcels_dseg.nii.gz ├── tpl-MNI152NLin6Asym_atlas-SubcorticalMerged_res-02_desc-Schaefer2018v0143x200ParcelsLabels_dseg.nii.gz ├── tpl-MNI152NLin6Asym_atlas-SubcorticalMerged_res-02_desc-Schaefer2018v0143x200Parcels_dseg.nii.gz ├── tpl-MNI152NLin6Asym_atlas-SubcorticalMerged_res-02_desc-Schaefer2018v0143x300ParcelsLabels_dseg.nii.gz ├── tpl-MNI152NLin6Asym_atlas-SubcorticalMerged_res-02_desc-Schaefer2018v0143x300Parcels_dseg.nii.gz ├── tpl-MNI152NLin6Asym_atlas-SubcorticalMerged_res-02_desc-Schaefer2018v0143x400ParcelsLabels_dseg.nii.gz ├── tpl-MNI152NLin6Asym_atlas-SubcorticalMerged_res-02_desc-Schaefer2018v0143x400Parcels_dseg.nii.gz ├── tpl-MNI152NLin6Asym_atlas-SubcorticalMerged_res-02_desc-Schaefer2018v0143x500ParcelsLabels_dseg.nii.gz ├── tpl-MNI152NLin6Asym_atlas-SubcorticalMerged_res-02_desc-Schaefer2018v0143x500Parcels_dseg.nii.gz ├── tpl-MNI152NLin6Asym_atlas-SubcorticalMerged_res-02_desc-Schaefer2018v0143x600ParcelsLabels_dseg.nii.gz ├── tpl-MNI152NLin6Asym_atlas-SubcorticalMerged_res-02_desc-Schaefer2018v0143x600Parcels_dseg.nii.gz ├── tpl-MNI152NLin6Asym_atlas-SubcorticalMerged_res-02_desc-Schaefer2018v0143x700ParcelsLabels_dseg.nii.gz ├── tpl-MNI152NLin6Asym_atlas-SubcorticalMerged_res-02_desc-Schaefer2018v0143x700Parcels_dseg.nii.gz ├── tpl-MNI152NLin6Asym_atlas-SubcorticalMerged_res-02_desc-Schaefer2018v0143x800ParcelsLabels_dseg.nii.gz ├── tpl-MNI152NLin6Asym_atlas-SubcorticalMerged_res-02_desc-Schaefer2018v0143x800Parcels_dseg.nii.gz ├── tpl-MNI152NLin6Asym_atlas-SubcorticalMerged_res-02_desc-Schaefer2018v0143x900ParcelsLabels_dseg.nii.gz ├── tpl-MNI152NLin6Asym_atlas-SubcorticalMerged_res-02_desc-Schaefer2018v0143x900Parcels_dseg.nii.gz ├── tpl-fsLR_hemi-L_den-32k_desc-nomedialwall_dparc.label.gii └── tpl-fsLR_hemi-R_den-32k_desc-nomedialwall_dparc.label.gii ├── Volumetric4S.ipynb ├── atlas-4S1056Parcels_dseg.tsv ├── atlas-4S156Parcels_dseg.tsv ├── atlas-4S256Parcels_dseg.tsv ├── atlas-4S356Parcels_dseg.tsv ├── atlas-4S456Parcels_dseg.tsv ├── atlas-4S556Parcels_dseg.tsv ├── atlas-4S656Parcels_dseg.tsv ├── atlas-4S756Parcels_dseg.tsv ├── atlas-4S856Parcels_dseg.tsv ├── atlas-4S956Parcels_dseg.tsv ├── cerebellum └── prepare_atlas.sh ├── docker_build └── Dockerfile ├── hippocampus_and_amygdala ├── prepare_atlas.sh └── split_regions.py ├── metadata └── generate_metadata.py ├── registration_scripts ├── upenn_NLin2009aSymTO2009cAsym.sh ├── upenn_NLin2009aSymTONLin6Asym.sh ├── upenn_NLin6SymTO2009cAsym.sh └── upenn_NLin6SymTONLin6Asym.sh ├── subcortex_merged ├── atlas-SubcorticalMerged_dseg.json ├── tpl-MNI152NLin2009cAsym_atlas-SubcorticalMerged_res-01_dseg.nii.gz ├── tpl-MNI152NLin2009cAsym_atlas-SubcorticalMerged_res-01_dseg.tsv ├── tpl-MNI152NLin6Asym_atlas-SubcorticalMerged_res-01_dseg.nii.gz └── tpl-MNI152NLin6Asym_atlas-SubcorticalMerged_res-01_dseg.tsv ├── subcortical_merged ├── tpl-MNI152NLin2009cAsym_atlas-SubcorticalMerged_res-01_dseg.nii.gz ├── tpl-MNI152NLin2009cAsym_atlas-SubcorticalMerged_res-01_dseg.tsv └── tpl-MNI152NLin6Asym_atlas-SubcorticalMerged_res-01_dseg.nii.gz ├── thalamus ├── make_labels_tsv.py └── prepare_atlas.sh ├── tpl-MNI152NLin2009cAsym_atlas-4S1056Parcels_res-01_dseg.nii.gz ├── tpl-MNI152NLin2009cAsym_atlas-4S156Parcels_res-01_dseg.nii.gz ├── tpl-MNI152NLin2009cAsym_atlas-4S256Parcels_res-01_dseg.nii.gz ├── tpl-MNI152NLin2009cAsym_atlas-4S356Parcels_res-01_dseg.nii.gz ├── tpl-MNI152NLin2009cAsym_atlas-4S456Parcels_res-01_dseg.nii.gz ├── tpl-MNI152NLin2009cAsym_atlas-4S556Parcels_res-01_dseg.nii.gz ├── tpl-MNI152NLin2009cAsym_atlas-4S656Parcels_res-01_dseg.nii.gz ├── tpl-MNI152NLin2009cAsym_atlas-4S756Parcels_res-01_dseg.nii.gz ├── tpl-MNI152NLin2009cAsym_atlas-4S856Parcels_res-01_dseg.nii.gz ├── tpl-MNI152NLin2009cAsym_atlas-4S956Parcels_res-01_dseg.nii.gz ├── tpl-MNI152NLin6Asym_atlas-4S1056Parcels_dseg.json ├── tpl-MNI152NLin6Asym_atlas-4S1056Parcels_res-01_dseg.nii.gz ├── tpl-MNI152NLin6Asym_atlas-4S156Parcels_dseg.json ├── tpl-MNI152NLin6Asym_atlas-4S156Parcels_res-01_dseg.nii.gz ├── tpl-MNI152NLin6Asym_atlas-4S256Parcels_dseg.json ├── tpl-MNI152NLin6Asym_atlas-4S256Parcels_res-01_dseg.nii.gz ├── tpl-MNI152NLin6Asym_atlas-4S356Parcels_dseg.json ├── tpl-MNI152NLin6Asym_atlas-4S356Parcels_res-01_dseg.nii.gz ├── tpl-MNI152NLin6Asym_atlas-4S456Parcels_dseg.json ├── tpl-MNI152NLin6Asym_atlas-4S456Parcels_res-01_dseg.nii.gz ├── tpl-MNI152NLin6Asym_atlas-4S556Parcels_dseg.json ├── tpl-MNI152NLin6Asym_atlas-4S556Parcels_res-01_dseg.nii.gz ├── tpl-MNI152NLin6Asym_atlas-4S656Parcels_dseg.json ├── tpl-MNI152NLin6Asym_atlas-4S656Parcels_res-01_dseg.nii.gz ├── tpl-MNI152NLin6Asym_atlas-4S756Parcels_dseg.json ├── tpl-MNI152NLin6Asym_atlas-4S756Parcels_res-01_dseg.nii.gz ├── tpl-MNI152NLin6Asym_atlas-4S856Parcels_dseg.json ├── tpl-MNI152NLin6Asym_atlas-4S856Parcels_res-01_dseg.nii.gz ├── tpl-MNI152NLin6Asym_atlas-4S956Parcels_dseg.json ├── tpl-MNI152NLin6Asym_atlas-4S956Parcels_res-01_dseg.nii.gz ├── tpl-fsLR_atlas-4S1056Parcels_den-91k_dseg.dlabel.nii ├── tpl-fsLR_atlas-4S1056Parcels_dseg.json ├── tpl-fsLR_atlas-4S156Parcels_den-91k_dseg.dlabel.nii ├── tpl-fsLR_atlas-4S156Parcels_dseg.json ├── tpl-fsLR_atlas-4S256Parcels_den-91k_dseg.dlabel.nii ├── tpl-fsLR_atlas-4S256Parcels_dseg.json ├── tpl-fsLR_atlas-4S356Parcels_den-91k_dseg.dlabel.nii ├── tpl-fsLR_atlas-4S356Parcels_dseg.json ├── tpl-fsLR_atlas-4S456Parcels_den-91k_dseg.dlabel.nii ├── tpl-fsLR_atlas-4S456Parcels_dseg.json ├── tpl-fsLR_atlas-4S556Parcels_den-91k_dseg.dlabel.nii ├── tpl-fsLR_atlas-4S556Parcels_dseg.json ├── tpl-fsLR_atlas-4S656Parcels_den-91k_dseg.dlabel.nii ├── tpl-fsLR_atlas-4S656Parcels_dseg.json ├── tpl-fsLR_atlas-4S756Parcels_den-91k_dseg.dlabel.nii ├── tpl-fsLR_atlas-4S756Parcels_dseg.json ├── tpl-fsLR_atlas-4S856Parcels_den-91k_dseg.dlabel.nii ├── tpl-fsLR_atlas-4S856Parcels_dseg.json ├── tpl-fsLR_atlas-4S956Parcels_den-91k_dseg.dlabel.nii ├── tpl-fsLR_atlas-4S956Parcels_dseg.json ├── transforms ├── tpl-MNI152NLin2009cAsym_from-MNI152NLin2009aSym_mode-image_xfm.h5 ├── tpl-MNI152NLin6Asym_from-MNI152NLin2009aSym_mode-image_xfm.h5 ├── tpl-MNI152NLin6Asym_from-MNI152NLin2009cAsym_mode-image_xfm.h5 └── tpl-MNI152NLin6Asym_from-MNI152NLin6Sym_mode-image_xfm.h5 └── utils.py /.circleci/config.yml: 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