Python API¶
This is the function reference of the ENIGMA TOOLBOX
enigmatoolbox.datasets
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ENIGMA datasets¶
Loads the ENIGMA example dataset (from one site - MICA-MNI Montreal; author: @saratheriver) |
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Outputs summary statistics for a given disorder (author: @saratheriver) |
Export functions¶
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Returns number of faces/triangles for a surface (author: @saratheriver) |
Returns vox2ras transform for a surface (author: @saratheriver) |
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Writes cifti file (authors: @NicoleEic, @saratheriver) |
Connectivity matrices¶
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Load functional connectivity data (author: @saratheriver) |
Load functional connectivity data (cortical + subcortical in one matrix; author: @saratheriver) |
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Load structural connectivity data (author: @saratheriver) |
Load structural connectivity data (cortical + subcortical in one matrix; author: @saratheriver) |
Gene co-expression data¶
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Fetch Allen Human Brain Atlas microarray expression data from all donors and all genes (author: @saratheriver) |
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Outputs names of GWAS-derived risk genes for a given disorder (author: @saratheriver) |
Surface templates¶
Load fsaverage5 surfaces (author: @saratheriver) |
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Load conte69 surfaces (author: @OualidBenkarim) |
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Load subcortical surfaces (author: @saratheriver) |
enigmatoolbox.cross_disorder
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enigmatoolbox.mesh
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Read/write functionality¶
Read surface data (author: @OualidBenkarim) |
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Write surface data (author: @OualidBenkarim) |
enigmatoolbox.permutation_testing
¶
Spin permutations¶
Spin permutation (author: @saratheriver) |
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Extract centroids of a cortical parcellation on a surface sphere (author: @saratheriver) |
Rotate parcellation (author: @saratheriver) |
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Generate a p-value for the spatial correlation between two parcellated cortical surface maps (author: @saratheriver) |
enigmatoolbox.plotting.surface_plotting
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Surface plotting¶
Plot cortical surface with lateral and medial views (authors: @OualidBenkarim, @saratheriver) |
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Plot subcortical surface with lateral and medial views (author: @saratheriver) |
Build plotter arranged according to the layout (author: @OualidBenkarim) |
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Plot surfaces arranged according to the layout (author: @OualidBenkarim) |
enigmatoolbox.utils
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Re-order subcortical data matrix¶
Re-order subcortical volume data alphabetically and by hemisphere (left then right; author: @saratheriver) |
Z-score data matrix¶
Z-score data relative to a given group (author: @saratheriver) |
Parcellation¶
Map data in source to target according to their labels (authors: @OualidBenkarim, @saratheriver) |
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Summarize data in values according to labels (author: @OualidBenkarim) |
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Map one value per subcortical area to surface vertices (author: @saratheriver) |