nispace.workflows.nimare_colocalization

nispace.workflows.nimare_colocalization(y, x='PET', z=None, x_collection=None, standardize='xz', space='MNI152NLin6Asym', data_space=None, parcellation_space=None, parcellation='Yan200', parcellation_labels=None, parcellation_hemi=['L', 'R'], y_covariates=None, colocalization_method=None, mc_method='meff', normalize_colocalizations=True, pooled_p=False, plot=True, binary_y=False, nimare_nulls=None, n_perm=10000, seed=None, n_proc=1, verbose=True, nispace_object=None, fetch_x_kwargs=None, init_kwargs=None, fit_kwargs=None, clean_y_kwargs=None, colocalize_kwargs=None, permute_kwargs=None, correct_p_kwargs=None, plot_kwargs=None, return_nispace_only=False)[source]

NiMARE colocalization workflow.

Convenience wrapper around colocalization() for Y maps derived from NiMARE meta-analyses (continuous ALE stat maps or binary cluster-coverage maps from get_binary_cluster_map()).

Sets the following defaults relative to colocalization():

  • background_value={"y": False} in fit_kwargs — zero-valued voxels in ALE maps are meaningful (no activation there), not missing data. Scoped to Y only: X (and Z, if given) keep the normal 'auto' background handling, since only Y is guaranteed to be an ALE/cluster-coverage map here.

  • maps_which="Y" in permute_kwargs when nimare_nulls is provided, so Y is permuted with coordinate-sampling null maps; otherwise "X"

For binary cluster maps also pass binary_y=True and colocalization_method="pearson".

Parameters:

  • y (NIfTI image, array-like, or list) – ALE stat map (result.get_map("stat")) or binary cluster-coverage map (from get_binary_cluster_map()).

  • x (str or array-like, default="PET") – Reference X maps. Same as colocalization().

  • colocalization_method (str or list, default=None) – Colocalization method. When None, defaults to "pearson" if binary_y=True (approximate point-biserial), otherwise "spearman".

  • binary_y (bool, default=False) – Set True when Y is a binary or fractional cluster-coverage map. Prevents z-scoring of Y and raises warnings for ranked methods or group permutation. See NiSpace for details.

  • nimare_nulls (dict or None, default=None) – Coordinate-sampling null maps from null_maps_from_nimare(). When provided, sets maps_nulls=nimare_nulls and maps_which="Y" in permute_kwargs so Y is permuted with the NiMARE null distribution. Explicit entries in permute_kwargs take precedence.

Returns:

  • nsp (NiSpace) – (when return_nispace_only=True)

  • colocs, p_values, pc_values, nsp (tuple) – Deprecated. Returned when return_nispace_only=False.

Notes

All other parameters are identical to colocalization().