AtlasesΒΆ

bids_atlas comes with support of a large collection of commonly used publicly available atlases. In the following you can find a respective list, indicating the atlas, the function to download it and its metadata.

AAL
Slice viewer
Function
from bids_atlas.datasets import get_AAL
AAL_atlas = get_AAL()
Meta-data
{
    "Name": "Automated Anatomical Labeling Atlas - SPM12 version",
    "Description": "PLEASE ADD",
    "BIDSVersion": "PLEASE ADD",
    "Curators": "PLEASE ADD",
    "HowToAcknowledge": "PLEASE ADD",
    "SourceDatasetsURLs": "PLEASE ADD",
    "License": "PLEASE ADD",
    "Funding": "PLEASE ADD",
    "ReferencesAndLinks": "PLEASE ADD",
    "Species": "PLEASE ADD",
    "DerivedFrom": "PLEASE ADD",
    "LevelType": "PLEASE ADD",
    "SpecialReference": "PLEASE ADD"
}
Destrieux
Slice viewer
Function
from bids_atlas.datasets import get_Destrieux
destrieux_atlas = get_Destrieux()
Meta-data
{
    "Name": "Destrieux cortical deterministic atlas - 2009 version",
    "Description": "Automatic parcellation of human cortical gyri and sulci using standard anatomical nomenclature",
    "BIDSVersion": "PLEASE ADD",
    "Curators": "PLEASE ADD",
    "HowToAcknowledge": "PLEASE ADD",
    "SourceDatasetsURLs": "PLEASE ADD",
    "License": "PLEASE ADD",
    "Funding": "PLEASE ADD",
    "ReferencesAndLinks": ["https://doi.org/10.1093/cercor/bhg087",
                        "https://doi.org/10.1016/j.neuroimage.2010.06.010"
                        ],
    "Species": "Human",
    "DerivedFrom": "PLEASE ADD",
    "LevelType": "PLEASE ADD",
    "SpecialReference": "PLEASE ADD"
}
Harvard-Oxford
deterministic version
Slice viewer
Function
from bids_atlas.datasets import get_HarvardOxford
HO_atlas = get_HarvardOxford(type='dseg', threshold='25')
Meta-data
{
    "Name": "Harvard-Oxford parcellations from FSL - deterministic version",
    "Description": "Harvard-Oxford parcellations from FSL",
    "BIDSVersion": "PLEASE ADD",
    "Curators": "PLEASE ADD",
    "HowToAcknowledge": "PLEASE ADD",
    "SourceDatasetsURLs": "PLEASE ADD",
    "License": "PLEASE ADD",
    "Funding": "PLEASE ADD",
    "ReferencesAndLinks": "PLEASE ADD",
    "Species": "PLEASE ADD",
    "DerivedFrom": "PLEASE ADD",
    "LevelType": "PLEASE ADD",
    "SpecialReference": "PLEASE ADD"
}
probabilistic version
Slice viewer
Function
from bids_atlas.datasets import get_HarvardOxford
HO_atlas = get_HarvardOxford(type='pseg')
Meta-data
{
    "Name": "Harvard-Oxford parcellations from FSL - probabilistic version",
    "Description": "Harvard-Oxford parcellations from FSL",
    "BIDSVersion": "PLEASE ADD",
    "Curators": "PLEASE ADD",
    "HowToAcknowledge": "PLEASE ADD",
    "SourceDatasetsURLs": "PLEASE ADD",
    "License": "PLEASE ADD",
    "Funding": "PLEASE ADD",
    "ReferencesAndLinks": "PLEASE ADD",
    "Species": "PLEASE ADD",
    "DerivedFrom": "PLEASE ADD",
    "LevelType": "PLEASE ADD",
    "SpecialReference": "PLEASE ADD"
}
Talairach
Gyrus level
Slice viewer
Function
from bids_atlas.datasets import get_talairach
talairach_atlas = get_talairach(level='gyrus')
Meta-data
{
    "Name": "Talairach Deterministic atlas",
    "Description": "PLEASE ADD",
    "BIDSVersion": "PLEASE ADD",
    "Curators": "PLEASE ADD",
    "HowToAcknowledge": "PLEASE ADD",
    "SourceDatasetsURLs": "PLEASE ADD",
    "License": "Unknown",
    "Funding": "PLEASE ADD",
    "ReferencesAndLinks": ["https://onlinelibrary.wiley.com/doi/abs/10.1002/1097-0193%28200007%2910%3A3%3C120%3A%3AAID-HBM30%3E3.0.CO%3B2-8",
                        "https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291097-0193%281997%295%3A4%3C238%3A%3AAID-HBM6%3E3.0.CO%3B2-4"],
    "Species": "Homo sapiens",
    "DerivedFrom": "PLEASE ADD",
    "LevelType": "PLEASE ADD",
    "SpecialReference": "PLEASE ADD"
}
Hemisphere level
Slice viewer
Function
from bids_atlas.datasets import get_talairach
talairach_atlas = get_talairach(level='hemisphere')
Meta-data
{
    "Name": "Talairach Deterministic atlas",
    "Description": "PLEASE ADD",
    "BIDSVersion": "PLEASE ADD",
    "Curators": "PLEASE ADD",
    "HowToAcknowledge": "PLEASE ADD",
    "SourceDatasetsURLs": "PLEASE ADD",
    "License": "Unknown",
    "Funding": "PLEASE ADD",
    "ReferencesAndLinks": ["https://onlinelibrary.wiley.com/doi/abs/10.1002/1097-0193%28200007%2910%3A3%3C120%3A%3AAID-HBM30%3E3.0.CO%3B2-8",
                        "https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291097-0193%281997%295%3A4%3C238%3A%3AAID-HBM6%3E3.0.CO%3B2-4"],
    "Species": "Homo sapiens",
    "DerivedFrom": "PLEASE ADD",
    "LevelType": "PLEASE ADD",
    "SpecialReference": "PLEASE ADD"
}
Lobe level
Slice viewer
Function
from bids_atlas.datasets import get_talairach
talairach_atlas = get_talairach(level='lobe')
Meta-data
{
    "Name": "Talairach Deterministic atlas",
    "Description": "PLEASE ADD",
    "BIDSVersion": "PLEASE ADD",
    "Curators": "PLEASE ADD",
    "HowToAcknowledge": "PLEASE ADD",
    "SourceDatasetsURLs": "PLEASE ADD",
    "License": "Unknown",
    "Funding": "PLEASE ADD",
    "ReferencesAndLinks": ["https://onlinelibrary.wiley.com/doi/abs/10.1002/1097-0193%28200007%2910%3A3%3C120%3A%3AAID-HBM30%3E3.0.CO%3B2-8",
                        "https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291097-0193%281997%295%3A4%3C238%3A%3AAID-HBM6%3E3.0.CO%3B2-4"],
    "Species": "Homo sapiens",
    "DerivedFrom": "PLEASE ADD",
    "LevelType": "PLEASE ADD",
    "SpecialReference": "PLEASE ADD"
}
Tissue level
Slice viewer
Function
from bids_atlas.datasets import get_talairach
talairach_atlas = get_talairach(level='tissue')
Meta-data
{
    "Name": "Talairach Deterministic atlas",
    "Description": "PLEASE ADD",
    "BIDSVersion": "PLEASE ADD",
    "Curators": "PLEASE ADD",
    "HowToAcknowledge": "PLEASE ADD",
    "SourceDatasetsURLs": "PLEASE ADD",
    "License": "Unknown",
    "Funding": "PLEASE ADD",
    "ReferencesAndLinks": ["https://onlinelibrary.wiley.com/doi/abs/10.1002/1097-0193%28200007%2910%3A3%3C120%3A%3AAID-HBM30%3E3.0.CO%3B2-8",
                        "https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291097-0193%281997%295%3A4%3C238%3A%3AAID-HBM6%3E3.0.CO%3B2-4"],
    "Species": "Homo sapiens",
    "DerivedFrom": "PLEASE ADD",
    "LevelType": "PLEASE ADD",
    "SpecialReference": "PLEASE ADD"
}
BA level
Slice viewer
Function
from bids_atlas.datasets import get_talairach
talairach_atlas = get_talairach(level='gyrus')
Meta-data
{
    "Name": "Talairach Deterministic atlas",
    "Description": "PLEASE ADD",
    "BIDSVersion": "PLEASE ADD",
    "Curators": "PLEASE ADD",
    "HowToAcknowledge": "PLEASE ADD",
    "SourceDatasetsURLs": "PLEASE ADD",
    "License": "Unknown",
    "Funding": "PLEASE ADD",
    "ReferencesAndLinks": ["https://onlinelibrary.wiley.com/doi/abs/10.1002/1097-0193%28200007%2910%3A3%3C120%3A%3AAID-HBM30%3E3.0.CO%3B2-8",
                        "https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291097-0193%281997%295%3A4%3C238%3A%3AAID-HBM6%3E3.0.CO%3B2-4"],
    "Species": "Homo sapiens",
    "DerivedFrom": "PLEASE ADD",
    "LevelType": "PLEASE ADD",
    "SpecialReference": "PLEASE ADD"
}
Juelich
deterministic version
Slice viewer
Function
from bids_atlas.datasets import get_Juelich
juelich_atlas = get_Juelich(type='dseg', threshold='25')
Meta-data
{
    "Name": "Juelich atlas",
    "Description": "PLEASE ADD",
    "BIDSVersion": "PLEASE ADD",
    "Curators": "PLEASE ADD",
    "HowToAcknowledge": "PLEASE ADD",
    "SourceDatasetsURLs": "PLEASE ADD",
    "License": "PLEASE ADD",
    "Funding": "PLEASE ADD",
    "ReferencesAndLinks": "PLEASE ADD",
    "Species": "PLEASE ADD",
    "DerivedFrom": "PLEASE ADD",
    "LevelType": "PLEASE ADD",
    "SpecialReference": "PLEASE ADD"
}
probabilistic version
Slice viewer
Function
from bids_atlas.datasets import get_Juelich
juelich_atlas = get_Juelich(type='pseg')
Meta-data
{
    "Name": "Juelich atlas",
    "Description": "PLEASE ADD",
    "BIDSVersion": "PLEASE ADD",
    "Curators": "PLEASE ADD",
    "HowToAcknowledge": "PLEASE ADD",
    "SourceDatasetsURLs": "PLEASE ADD",
    "License": "PLEASE ADD",
    "Funding": "PLEASE ADD",
    "ReferencesAndLinks": "PLEASE ADD",
    "Species": "PLEASE ADD",
    "DerivedFrom": "PLEASE ADD",
    "LevelType": "PLEASE ADD",
    "SpecialReference": "PLEASE ADD"
}