Reference API

neuromaps.datasets - Dataset fetchers

Functions for fetching datasets.

Functions to show all available annotations

available_annotations([source, desc, space, ...])	List datasets available via fetch_annotation().
available_tags([return_restricted])	Return available tags for querying annotations.

Functions to fetch and describe the annotations

fetch_annotation(*[, source, desc, space, ...])	Download files for brain annotations matching requested variables.
describe_annotations(annots[, format])	Return detailed descriptions for annotations as a pandas dataframe.

Functions to fetch the atlases

fetch_atlas(atlas, density[, url, data_dir, ...])	Fetch specified atlas and density.
fetch_civet([density, url, data_dir, verbose])	Fetch CIVET surface atlas.
fetch_fsaverage([density, url, data_dir, ...])	Fetch fsaverage surface atlas.
fetch_fslr([density, url, data_dir, verbose])	Fetch fsLR surface atlas.
fetch_mni152([density, url, data_dir, verbose])	Fetch MNI152 atlas.
fetch_regfusion(atlas[, url, data_dir, verbose])	Fetch regfusion inputs for mapping MNI152 to specified surface atlas.
fetch_all_atlases([data_dir, verbose])	Fetch (and cache) all available atlases.
get_atlas_dir(atlas[, data_dir])	Return filepath to specified atlas.

neuromaps.images - Image and surface handling

Functions for operating on images + surfaces.

Functions to load the images and surfaces

load_gifti(img)	Load gifti file img.
load_nifti(img)	Load nifti file img.

Functions to convert surfaces to GIFTI format

relabel_gifti(parcellation[, background, offset])	Update GIFTI images so label IDs are consecutive across hemispheres.
annot_to_gifti(parcellation[, background])	Convert FreeSurfer-style annotation parcellation files to GIFTI images.
dlabel_to_gifti(parcellation)	Convert CIFTI dlabel file to GIFTI images.
obj_to_gifti(obj[, fn])	Convert CIVET obj surface file to GIFTI format.
fssurf_to_gifti(surf[, fn])	Convert FreeSurfer surf surface file to GIFTI format.
fsmorph_to_gifti(morph[, fn, modifier])	Convert FreeSurfer morph data file to GIFTI format.

Functions to work with surfaces

average_surfaces(*surfs)	Generate average surface from input surfs.
interp_surface(data, src, trg[, method])	Interpolate data on src surface to trg surface.
vertex_areas(surface)	Calculate vertex areas from surface file.

neuromaps.nulls - Null models

Functions for computing null models.

Spatial permutation null models (for surface images only)

alexander_bloch(data[, atlas, density, ...])	Generate null maps from data using method from [SN1].
vazquez_rodriguez(data[, atlas, density, ...])	Generate null maps from data using method from [SN1].
vasa(data[, atlas, density, parcellation, ...])	Generate null maps for parcellated data using method from [SN2].
hungarian(data[, atlas, density, ...])	Generate null maps for parcellated data using the Hungarian method ([SN3]).
baum(data[, atlas, density, parcellation, ...])	Generate null maps for parcellated data using method from [SN4].
cornblath(data[, atlas, density, ...])	Generate null maps for parcellated data using method from [SN5].

Parametric spatial null models (for volumetric and surface images)

burt2018(data[, atlas, density, ...])	Generate null maps for data using method from [SN6].
burt2020(data[, atlas, density, ...])	Generate null maps for data using method from [SN7] and [SN8].
moran(data[, atlas, density, parcellation, ...])	Generate null maps for data using method from [SN9].

neuromaps.parcellate - Parcellation utilities

Functionality for parcellating data.

Parcellater(parcellation, space[, ...])

Class for parcellating arbitrary volumetric / surface data.

neuromaps.plotting - Plotting functions

Functionality for plotting.

plot_surf_template(data, template, density)

Plot data on template surface.

neuromaps.points - Triangle mesh utilities

Functions for working with triangle meshes + surfaces.

make_surf_graph(vertices, faces[, mask])	Construct adjacency graph from surf.
get_surface_distance(surface[, ...])	Calculate surface distance for vertices in surface.

neuromaps.resampling - Resampling workflows

Functions for comparing data.

resample_images(src, trg, src_space, trg_space)

Resample images src and trg to same space/density with resampling method.

neuromaps.stats - Statistical functions

Functions for statistical analyses.

compare_images(src, trg[, metric, ...])	Compare images src and trg.
permtest_metric(a, b[, metric, n_perm, ...])	Generate non-parameteric p-value of a and b for metric.

neuromaps.transforms - Transformations between spaces

Functionality for transforming files between spaces.

Volume-to-surface transformations

mni152_to_civet(img[, civet_density, method])	Project img in MNI152 space to CIVET surface.
mni152_to_fsaverage(img[, fsavg_density, method])	Project img in MNI152 space to fsaverage surface.
mni152_to_fslr(img[, fslr_density, method])	Project img in MNI152 space to fsLR surface.

Volume-to-volume transformations

mni152_to_mni152(img[, target, method])

Resample img to target image (if supplied) or target resolution.

Surface-to-surface transformations

civet_to_fslr(data[, target_density, hemi, ...])	Resample data on CIVET surface to the fsLR surface.
fslr_to_civet(data[, target_density, hemi, ...])	Resample data on fsLR surface to the CIVET surface.
civet_to_fsaverage(data[, target_density, ...])	Resample data on CIVET surface to the fsaverage surface.
fsaverage_to_civet(data[, target_density, ...])	Resample data on fsaverage surface to the CIVET surface.
civet_to_civet(data[, target_density, hemi, ...])	Resample data on CIVET surface to new density.
fslr_to_fsaverage(data[, target_density, ...])	Resample data on fsLR surface to the fsaverage surface.
fsaverage_to_fslr(data[, target_density, ...])	Resample data on fsaverage surface to the fsLR surface.
fslr_to_fslr(data[, target_density, hemi, ...])	Resample data on fsLR surface to new density.
fsaverage_to_fsaverage(data[, ...])	Resample data on fsaverage surface to new density.