Reference API

List of modules

neuromaps.datasets - Dataset fetchers

Functions for fetching datasets

neuromaps.datasets.fetch_atlas(atlas, density)

Fetches specified atlas and density

neuromaps.datasets.fetch_civet([density, ...])

Fetches CIVET surface atlas

neuromaps.datasets.fetch_fsaverage([...])

Fetches fsaverage surface atlas

neuromaps.datasets.fetch_fslr([density, ...])

Fetches fsLR surface atlas

neuromaps.datasets.fetch_mni152([density, ...])

Fetches MNI152 atlas

neuromaps.datasets.fetch_regfusion(atlas[, ...])

Fetches regfusion inputs for mapping MNI152 to specified surface atlas

neuromaps.datasets.fetch_all_atlases([...])

Fetches (and caches) all available atlases

neuromaps.datasets.available_annotations([...])

Lists datasets available via fetch_annotation()

neuromaps.datasets.available_tags([...])

Returns available tags for querying annotations

neuromaps.datasets.fetch_annotation(*[, ...])

Downloads files for brain annotations matching requested variables

neuromaps.datasets.get_atlas_dir(atlas[, ...])

Returns filepath to specified atlas

neuromaps.datasets.upload_annotation(files, user)

Workflow for contributing new brain annotation files to neuromaps

neuromaps.images - Image and surface handling

Functions for operating on images + surfaces

neuromaps.images.load_gifti(img)

Loads gifti file img

neuromaps.images.load_nifti(img)

Loads nifti file img.

neuromaps.images.average_surfaces(*surfs)

Generates average surface from input surfs

neuromaps.images.interp_surface(data, src, trg)

Interpolate data on src surface to trg surface

neuromaps.images.vertex_areas(surface)

Calculates vertex areas from surface file

neuromaps.images.relabel_gifti(parcellation)

Updates GIFTI images so label IDs are consecutive across hemispheres

neuromaps.images.annot_to_gifti(parcellation)

Converts FreeSurfer-style annotation parcellation files to GIFTI images

neuromaps.images.dlabel_to_gifti(parcellation)

Converts CIFTI dlabel file to GIFTI images

neuromaps.images.obj_to_gifti(obj[, fn])

Converts CIVET obj surface file to GIFTI format

neuromaps.images.fssurf_to_gifti(surf[, fn])

Converts FreeSurfer surf surface file to GIFTI format

neuromaps.images.fsmorph_to_gifti(morph[, ...])

Converts FreeSurfer morph data file to GIFTI format

neuromaps.nulls - Null models

Functions for computing null models

neuromaps.nulls.alexander_bloch(data[, ...])

Generates null maps from data using method from [SN1]

neuromaps.nulls.vazquez_rodriguez(data[, ...])

Generates null maps from data using method from [SN1]

neuromaps.nulls.vasa(data[, atlas, density, ...])

Generates null maps for parcellated data using method from [SN2]

neuromaps.nulls.hungarian(data[, atlas, ...])

Generates null maps for parcellated data using the Hungarian method ([SN3])

neuromaps.nulls.baum(data[, atlas, density, ...])

Generates null maps for parcellated data using method from [SN4]

neuromaps.nulls.cornblath(data[, atlas, ...])

Generates null maps for parcellated data using method from [SN5]

neuromaps.nulls.burt2018(data[, atlas, ...])

Generates null maps for data using method from [SN6]

neuromaps.nulls.burt2020(data[, atlas, ...])

Generates null maps for data using method from [SN7] and [SN8]

neuromaps.nulls.moran(data[, atlas, ...])

Generates null maps for data using method from [SN9]

neuromaps.parcellate - Parcellation utilities

Functionality for parcellating data

neuromaps.parcellate.Parcellater(...[, ...])

Class for parcellating arbitrary volumetric / surface data

neuromaps.plotting - Plotting functions

Functionality for plotting

neuromaps.plotting.plot_surf_template(data, ...)

Plots data on template surface

neuromaps.points - Triangle mesh utilites

Functions for working with triangle meshes + surfaces

neuromaps.points.make_surf_graph(vertices, faces)

Constructs adjacency graph from surf.

neuromaps.points.get_surface_distance(surface)

Calculates surface distance for vertices in surface

neuromaps.resampling - Resampling workflows

Functions for comparing data

neuromaps.resampling.resample_images(src, ...)

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

neuromaps.stats - Statistical functions

Functions for statistical analyses

neuromaps.stats.compare_images(src, trg[, ...])

Compares images src and trg

neuromaps.stats.permtest_metric(a, b[, ...])

Generates non-parameteric p-value of a and b for metric

neuromaps.transforms - Transformations between spaces

Functionality for transforming files between spaces

neuromaps.transforms.mni152_to_civet(img[, ...])

Projects img in MNI152 space to CIVET surface

neuromaps.transforms.mni152_to_fsaverage(img)

Projects img in MNI152 space to fsaverage surface

neuromaps.transforms.mni152_to_fslr(img[, ...])

Projects img in MNI152 space to fsLR surface

neuromaps.transforms.mni152_to_mni152(img[, ...])

Resamples img to target image (if supplied) or target resolution

neuromaps.transforms.civet_to_fslr(data[, ...])

Resamples data on CIVET surface to the fsLR surface

neuromaps.transforms.fslr_to_civet(data[, ...])

Resamples data on fsLR surface to the CIVET surface

neuromaps.transforms.civet_to_fsaverage(data)

Resamples data on CIVET surface to the fsaverage surface

neuromaps.transforms.fsaverage_to_civet(data)

Resamples data on fsaverage surface to the CIVET surface

neuromaps.transforms.civet_to_civet(data[, ...])

Resamples data on CIVET surface to new density

neuromaps.transforms.fslr_to_fsaverage(data)

Resamples data on fsLR surface to the fsaverage surface

neuromaps.transforms.fsaverage_to_fslr(data)

Resamples data on fsaverage surface to the fsLR surface

neuromaps.transforms.fslr_to_fslr(data[, ...])

Resamples data on fsLR surface to new density

neuromaps.transforms.fsaverage_to_fsaverage(data)

Resamples data on fsaverage surface to new density