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¶

von Economo-Koskinas stratification¶

`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)