Python API¶
This is the function reference of the ENIGMA TOOLBOX
enigmatoolbox.datasets¶
ENIGMA datasets¶
enigmatoolbox.datasets.load_example_data() |
Loads the ENIGMA example dataset (from one site - MICA-MNI Montreal; author: @saratheriver) |
enigmatoolbox.datasets.load_summary_stats([…]) |
Outputs summary statistics for a given disorder (author: @saratheriver) |
Export functions¶
enigmatoolbox.datasets.nfaces(surface_name, …) |
Returns number of faces/triangles for a surface (author: @saratheriver) |
enigmatoolbox.datasets.getaffine(…) |
Returns vox2ras transform for a surface (author: @saratheriver) |
enigmatoolbox.datasets.write_cifti(data[, …]) |
Writes cifti file (authors: @NicoleEic, @saratheriver) |
Connectivity matrices¶
enigmatoolbox.datasets.load_fc([parcellation]) |
Load functional connectivity data (author: @saratheriver) |
enigmatoolbox.datasets.load_fc_as_one([…]) |
Load functional connectivity data (cortical + subcortical in one matrix; author: @saratheriver) |
enigmatoolbox.datasets.load_sc([parcellation]) |
Load structural connectivity data (author: @saratheriver) |
enigmatoolbox.datasets.load_sc_as_one([…]) |
Load structural connectivity data (cortical + subcortical in one matrix; author: @saratheriver) |
Gene co-expression data¶
enigmatoolbox.datasets.fetch_ahba([csvfile]) |
Fetch Allen Human Brain Atlas microarray expression data from all donors and all genes (author: @saratheriver) |
enigmatoolbox.datasets.risk_genes([disorder]) |
Outputs names of GWAS-derived risk genes for a given disorder (author: @saratheriver) |
Surface templates¶
enigmatoolbox.datasets.load_fsa5([…]) |
Load fsaverage5 surfaces (author: @saratheriver) |
enigmatoolbox.datasets.load_conte69([…]) |
Load conte69 surfaces (author: @OualidBenkarim) |
enigmatoolbox.datasets.load_subcortical([…]) |
Load subcortical surfaces (author: @saratheriver) |
enigmatoolbox.cross_disorder¶
Cross-disorder effect¶
enigmatoolbox.cross_disorder.cross_disorder_effect([…]) |
Cross-disorder effect (authors: @boyongpark, @saratheriver) |
enigmatoolbox.mesh¶
Read/write functionality¶
enigmatoolbox.mesh.mesh_io.read_surface(ipth) |
Read surface data (author: @OualidBenkarim) |
enigmatoolbox.mesh.mesh_io.write_surface(…) |
Write surface data (author: @OualidBenkarim) |
enigmatoolbox.permutation_testing¶
Spin permutations¶
enigmatoolbox.permutation_testing.spin_test(…) |
Spin permutation (author: @saratheriver) |
enigmatoolbox.permutation_testing.centroid_extraction_sphere(…) |
Extract centroids of a cortical parcellation on a surface sphere (author: @saratheriver) |
enigmatoolbox.permutation_testing.rotate_parcellation(…) |
Rotate parcellation (author: @saratheriver) |
enigmatoolbox.permutation_testing.perm_sphere_p(x, …) |
Generate a p-value for the spatial correlation between two parcellated cortical surface maps (author: @saratheriver) |
Shuf permutations¶
enigmatoolbox.permutation_testing.shuf_test(…) |
Shuf permuation (author: @saratheriver) |
enigmatoolbox.plotting.surface_plotting¶
Surface plotting¶
enigmatoolbox.plotting.surface_plotting.plot_cortical([…]) |
Plot cortical surface with lateral and medial views (authors: @OualidBenkarim, @saratheriver) |
enigmatoolbox.plotting.surface_plotting.plot_subcortical([…]) |
Plot subcortical surface with lateral and medial views (author: @saratheriver) |
enigmatoolbox.plotting.surface_plotting.build_plotter(…) |
Build plotter arranged according to the layout (author: @OualidBenkarim) |
enigmatoolbox.plotting.surface_plotting.plot_surf(…) |
Plot surfaces arranged according to the layout (author: @OualidBenkarim) |
enigmatoolbox.histology¶
BigBrain stratification¶
enigmatoolbox.histology.bb_moments_raincloud |
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enigmatoolbox.histology.bb_gradient_plot |
von Economo-Koskinas stratification¶
enigmatoolbox.histology.economo_koskinas_spider |
enigmatoolbox.utils¶
Re-order subcortical data matrix¶
enigmatoolbox.utils.useful.reorder_sctx(data) |
Re-order subcortical volume data alphabetically and by hemisphere (left then right; author: @saratheriver) |
Z-score data matrix¶
enigmatoolbox.utils.useful.zscore_matrix(…) |
Z-score data relative to a given group (author: @saratheriver) |
Parcellation¶
enigmatoolbox.utils.parcellation.parcel_to_surface(…) |
Map data in source to target according to their labels (authors: @OualidBenkarim, @saratheriver) |
enigmatoolbox.utils.parcellation.surface_to_parcel(…) |
Summarize data in values according to labels (author: @OualidBenkarim) |
enigmatoolbox.utils.parcellation.subcorticalvertices([…]) |
Map one value per subcortical area to surface vertices (author: @saratheriver) |