siibra.livequeries.bigbrain

Matches BigBrain intensity profiles extracted by Wagstyl et al. to volumes.

Classes

BigBrain1MicronPatchQuery	Sample approximately orthogonal cortical image patches
BigBrainProfileQuery	Helper class that provides a standard way to create an ABC using
LayerwiseBigBrainIntensityQuery	Helper class that provides a standard way to create an ABC using
WagstylProfileLoader

Module Contents

class siibra.livequeries.bigbrain.BigBrain1MicronPatchQuery(lower_threshold=0.0)

Sample approximately orthogonal cortical image patches from BigBrain 1 micron sections, guided by an image volume in a supported reference space providing. The image volume is used as a weighted mask to extract patches along the cortical midsurface with nonzero weights in the input image. An optional lower_threshold can be used to narrow down the search The weight is stored with the resulting features.

query(concept: siibra.core.structure.BrainStructure, **kwargs) → List[siibra.features.image.BigBrain1MicronPatch]

layermap

lower_threshold = 0.0

class siibra.livequeries.bigbrain.BigBrainProfileQuery

Helper class that provides a standard way to create an ABC using inheritance.

query(concept: siibra.core.structure.BrainStructure, **kwargs) → List[siibra.features.tabular.bigbrain_intensity_profile.BigBrainIntensityProfile]

class siibra.livequeries.bigbrain.LayerwiseBigBrainIntensityQuery

Helper class that provides a standard way to create an ABC using inheritance.

query(concept: siibra.core.structure.BrainStructure, **kwargs) → List[siibra.features.tabular.layerwise_bigbrain_intensities.LayerwiseBigBrainIntensities]

class siibra.livequeries.bigbrain.WagstylProfileLoader

__len__()

DATASET

MESH_FILE_LEFT = 'data/gray_left_327680.surf.gii'

PROFILES_FILE_LEFT = 'data/profiles_left.npy'

REPO = 'https://github.com/kwagstyl/cortical_layers_tutorial/raw/main'

THICKNESSES_FILE_LEFT = 'data/thicknesses_left.npy'

property profile_labels