Tools Index

Plotting

surfplot_canonical_foldunfold(cdata[, ...])

Plots canonical folded and unfolded surfaces for hippocampus and dentate gyrus. :param cdata: Array with the shape Vx2xF, where V is the number of vertices (including DG unless specified), 2 is the number of hemispheres (unless specified), and F is the number of rows/features. :type cdata: numpy.ndarray :param hemis: List of hemispheres to visualize. Default is ['L', 'R']. :type hemis: list of str, optional :param labels: List of labels for different structures. Default is ['hipp', 'dentate']. :type labels: list of str, optional :param unfoldAPrescale: Whether to pre-scale the anterior-posterior axis during unfolding. Default is False. :type unfoldAPrescale: bool, optional :param den: Density parameter for surface plot. Default is '0p5mm'. :type den: str, optional :param tighten_cwindow: Whether to tighten the color window for the surface plot. Default is False. :type tighten_cwindow: bool, optional :param resourcesdir: Directory path containing additional resources. Default is the value of resourcesdir. :type resourcesdir: str, optional :param size: Size of the surface plot. Default is [350, 300]. :type size: list of int, optional :param **qwargs: Additional keyword arguments for customization. See https://brainspace.readthedocs.io/en/latest/generated/brainspace.plotting.surface_plotting.plot_surf.html#brainspace.plotting.surface_plotting.plot_surf :type **qwargs: dict, optional.

surfplot_sub_foldunfold(hippunfold_dir, sub, ...)

Plots subject-specific folded and unfolded surfaces (hipp/dentate; folded/unfolded).

Stats

`spin_test`(imgfix, imgperm[, nperm, metric, ...])	Permutation testing of unfolded hippocampus maps.
`moran_test`(imgfix, imgperm[, nperm, metric, ...])	Moran Spectral Randomization Moran Spectral Randomization (MSR) computes Moran’s I, a metric for spatial auto-correlation and generates normally distributed data with similar auto-correlation.
`eigenstrapping`(imgfix, imgperm[, nperm, ...])	Awesome new tool at https://www.biorxiv.org/content/10.1101/2024.02.07.579070v1.abstract Generates null models of spatial maps by rotating geometric eigenmodes.
`contextualize2D`(taskMaps[, n_topComparison, ...])	Compares the present maps to thoes in the inital HippoMaps release

Fetcher

`tree_osf_hashes`(repoID, name_hashes, ...)	Recursively fetch file hashes from the OSF repository.
`get_map`([repo, Dataset, Method, Modality, ...])	Search and load data from OSF with specified parameters.

Utils

`surfdat_smooth`(F, cdata[, iters, cores])	Smooths surface data across neighboring vertices.
`profile_align`(P[, patchdist, V, F, maxroll])	Aligns microstructural profiles in the depth direction across a set of surfaces.
`laplace_solver`(faces, init[, maxiters, ...])	Solves the Laplace equation along vertices of a surface.
`density_interp`(indensity, outdensity, cdata, ...)	Interpolates data from one surface density onto another via unfolded space.
`surface_to_volume`(surf_data, indensity, ...)	Labels voxels using data on a folded/unfolded surface and native space coordinates images.