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 |
|
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) |