Matlab API


enigma datasets

load_example_data() Loads the ENIGMA example dataset (from one site - MICA-MNI Montreal; author: @saratheriver)
load_summary_stats(disorder) Outputs summary statistics for a given disorder (author: @saratheriver)

import / export

nfaces(surface_name, hemisphere) Returns number of faces/triangles for a surface (author: @saratheriver)
getaffine(surface_name, hemisphere) Returns vox2ras transform for a surface (author: @saratheriver)
write_cifti(data, varargin) Writes cifti file (authors: @NicoleEic, @saratheriver)

connectivity matrices

load_fc() Load functional connectivity data (author: @saratheriver)
load_fc_as_one() Load functional connectivity data (cortical + subcortical in one matrix; author: @saratheriver)
load_sc() Load structural connectivity data (author: @saratheriver)
load_sc_as_one() Load structural connectivity data (cortical + subcortical in one matrix; author: @saratheriver)

gene co-expression data

fetch_ahba() Fetch Allen Human Brain Atlas microarray expression data from all donors and all genes (author: @saratheriver)
risk_genes(disease) Outputs names of GWAS-derived risk genes for a given disorder

cross-disorder effect

cross_disorder_effect() Cross-disorder effect (authors: @boyongpark, @saratheriver)

spin permutations

spin_test(map1, map2, varargin) Spin permutation (author: @saratheriver)
centroid_extraction_sphere(sphere_coords, annotfile) Extract centroids of a cortical parcellation on a surface sphere (authors: @frantisekvasa, @saratheriver)
rotate_parcellation(coord_l, coord_r, nrot) Rotate parcellation (authors: @frantisekvasa, @saratheriver)
perm_sphere_p(x, y, perm_id, corr_type) Generate a p-value for the spatial correlation between two parcellated cortical surface maps (authors: @frantisekvasa, @saratheriver)

shuf permutations

shuf_test(map1, map2, varargin) Shuf permuation (author: @saratheriver)

surface plotting

plot_cortical(data, varargin) Plot cortical surface with lateral and medial views (authors: @MICA-MNI, @saratheriver)
plot_subcortical(data, varargin) Plot subcortical surface with lateral and medial views (author: @saratheriver)

histology

bb_moments_raincloud(region_idx, title) Stratify regional data according to BigBrain statistical moments (authors: @caseypaquola, @saratheriver)
bb_gradient_plot(data, varargin) Stratify parcellated data according to the BigBrain gradient (authors: @caseypaquola, @saratheriver)
economo_koskinas_spider(parcel_data, varargin) Stratify parcellated data according to von Economo-Koskinas cytoarchitectonic classes (authors: @caseypaquola, @saratheriver)

re-order subcortical data matrix

reorder_sctx(data) Re-order subcortical volume data alphabetically and by hemisphere (left then rightl; author: @saratheriver)

z-score data matrix

zscore_matrix(data, group, controlCode) Z-score data relative to a given group (author: @saratheriver)

parcellation

parcel_to_surface(parcel_data, parcellation, fill) Map parcellated data to the surface (authors : @MICA-MNI, @saratheriver)
surface_to_parcel(surf_data, parcellation) Map surface data to a parcellation (authors : @MICA-MNI, @saratheriver)