nimare 0.4.2__py3-none-any.whl

nimare/meta/cbma/mkda.py

@@ -0,0 +1,1361 @@
+"""CBMA methods from the multilevel kernel density analysis (MKDA) family."""
+
+import logging
+
+import nibabel as nib
+import numpy as np
+import sparse
+from joblib import Memory, Parallel, delayed
+from pymare.stats import fdr
+from scipy import ndimage
+from scipy.stats import chi2
+from tqdm.auto import tqdm
+
+from nimare import _version
+from nimare.meta.cbma.base import CBMAEstimator, PairwiseCBMAEstimator
+from nimare.meta.kernel import KDAKernel, MKDAKernel
+from nimare.meta.utils import _calculate_cluster_measures
+from nimare.stats import null_to_p, one_way, two_way
+from nimare.transforms import p_to_z
+from nimare.utils import _check_ncores, vox2mm
+
+LGR = logging.getLogger(__name__)
+__version__ = _version.get_versions()["version"]
+
+
+class MKDADensity(CBMAEstimator):
+    r"""Multilevel kernel density analysis- Density analysis.
+
+    The MKDA density method was originally introduced in :footcite:t:`wager2007meta`.
+
+    .. versionchanged:: 0.2.1
+
+        - New parameters: ``memory`` and ``memory_level`` for memory caching.
+
+    .. versionchanged:: 0.0.12
+
+        - Use a 4D sparse array for modeled activation maps.
+
+    Parameters
+    ----------
+    kernel_transformer : :obj:`~nimare.meta.kernel.KernelTransformer`, optional
+        Kernel with which to convolve coordinates from dataset. Default is
+        :class:`~nimare.meta.kernel.MKDAKernel`.
+    null_method : {"approximate", "montecarlo"}, optional
+        Method by which to determine uncorrected p-values. The available options are
+
+        ======================= =================================================================
+        "approximate" (default) Build a histogram of summary-statistic values and their
+                                expected frequencies under the assumption of random spatial
+                                associated between studies, via a weighted convolution.
+
+                                This method is much faster, but slightly less accurate.
+        "montecarlo"            Perform a large number of permutations, in which the coordinates
+                                in the studies are randomly drawn from the Estimator's brain mask
+                                and the full set of resulting summary-statistic values are
+                                incorporated into a null distribution (stored as a histogram for
+                                memory reasons).
+
+                                This method is must slower, and is only slightly more accurate.
+        ======================= =================================================================
+
+    n_iters : int, default=5000
+        Number of iterations to use to define the null distribution.
+        This is only used if ``null_method=="montecarlo"``.
+        Default is 5000.
+    memory : instance of :class:`joblib.Memory`, :obj:`str`, or :class:`pathlib.Path`
+        Used to cache the output of a function. By default, no caching is done.
+        If a :obj:`str` is given, it is the path to the caching directory.
+    memory_level : :obj:`int`, default=0
+        Rough estimator of the amount of memory used by caching.
+        Higher value means more memory for caching. Zero means no caching.
+    n_cores : :obj:`int`, optional
+        Number of cores to use for parallelization.
+        This is only used if ``null_method=="montecarlo"``.
+        If <=0, defaults to using all available cores.
+        Default is 1.
+    **kwargs
+        Keyword arguments. Arguments for the kernel_transformer can be assigned
+        here, with the prefix '\kernel__' in the variable name.
+
+    Attributes
+    ----------
+    masker : :class:`~nilearn.input_data.NiftiMasker` or similar
+        Masker object.
+    inputs_ : :obj:`dict`
+        Inputs to the Estimator. For CBMA estimators, there is only one key: coordinates.
+        This is an edited version of the dataset's coordinates DataFrame.
+    null_distributions_ : :obj:`dict` of :class:`numpy.ndarray`
+        Null distributions for the uncorrected summary-statistic-to-p-value conversion and any
+        multiple-comparisons correction methods.
+        Entries are added to this attribute if and when the corresponding method is applied.
+
+        If ``null_method == "approximate"``:
+
+            -   ``histogram_means``: Array of mean value per experiment.
+            -   ``histogram_bins``: Array of bin centers for the null distribution histogram,
+                ranging from zero to the maximum possible summary statistic value for the Dataset.
+            -   ``histweights_corr-none_method-approximate``: Array of weights for the null
+                distribution histogram, with one value for each bin in ``histogram_bins``.
+
+        If ``null_method == "montecarlo"``:
+
+            -   ``histogram_bins``: Array of bin centers for the null distribution histogram,
+                ranging from zero to the maximum possible summary statistic value for the Dataset.
+            -   ``histweights_corr-none_method-montecarlo``: Array of weights for the null
+                distribution histogram, with one value for each bin in ``histogram_bins``.
+                These values are derived from the full set of summary statistics from each
+                iteration of the Monte Carlo procedure.
+            -   ``histweights_level-voxel_corr-fwe_method-montecarlo``: Array of weights for the
+                voxel-level FWE-correction null distribution, with one value for each bin in
+                ``histogram_bins``. These values are derived from the maximum summary statistic
+                from each iteration of the Monte Carlo procedure.
+
+        If :meth:`correct_fwe_montecarlo` is applied:
+
+            -   ``values_level-voxel_corr-fwe_method-montecarlo``: The maximum summary statistic
+                value from each Monte Carlo iteration. An array of shape (n_iters,).
+            -   ``values_desc-size_level-cluster_corr-fwe_method-montecarlo``: The maximum cluster
+                size from each Monte Carlo iteration. An array of shape (n_iters,).
+            -   ``values_desc-mass_level-cluster_corr-fwe_method-montecarlo``: The maximum cluster
+                mass from each Monte Carlo iteration. An array of shape (n_iters,).
+
+    Notes
+    -----
+    The MKDA density algorithm is also implemented in MATLAB at
+    https://github.com/canlab/Canlab_MKDA_MetaAnalysis.
+
+    Available correction methods: :func:`MKDADensity.correct_fwe_montecarlo`
+
+    References
+    ----------
+    .. footbibliography::
+    """
+
+    def __init__(
+        self,
+        kernel_transformer=MKDAKernel,
+        null_method="approximate",
+        n_iters=5000,
+        memory=Memory(location=None, verbose=0),
+        memory_level=0,
+        n_cores=1,
+        **kwargs,
+    ):
+        if not (isinstance(kernel_transformer, MKDAKernel) or kernel_transformer == MKDAKernel):
+            LGR.warning(
+                f"The KernelTransformer being used ({kernel_transformer}) is not optimized "
+                f"for the {type(self).__name__} algorithm. "
+                "Expect suboptimal performance and beware bugs."
+            )
+
+        # Add kernel transformer attribute and process keyword arguments
+        super().__init__(
+            kernel_transformer=kernel_transformer,
+            memory=memory,
+            memory_level=memory_level,
+            **kwargs,
+        )
+        self.null_method = null_method
+        self.n_iters = None if null_method == "approximate" else n_iters or 5000
+        self.n_cores = _check_ncores(n_cores)
+        self.dataset = None
+
+    def _generate_description(self):
+        """Generate a description of the fitted Estimator.
+
+        Returns
+        -------
+        str
+            Description of the Estimator.
+        """
+        if self.null_method == "montecarlo":
+            null_method_str = (
+                "a Monte Carlo-based null distribution, in which dataset coordinates were "
+                "randomly drawn from the analysis mask and the full set of ALE values were "
+                f"retained, using {self.n_iters} iterations"
+            )
+        else:
+            null_method_str = "an approximate null distribution"
+
+        description = (
+            "A multilevel kernel density (MKDA) meta-analysis \\citep{wager2007meta} was "
+            "performed was performed with NiMARE "
+            f"{__version__} "
+            "(RRID:SCR_017398; \\citealt{Salo2023}), using a(n) "
+            f"{self.kernel_transformer.__class__.__name__.replace('Kernel', '')} kernel. "
+            f"{self.kernel_transformer._generate_description()} "
+            f"Summary statistics (OF values) were converted to p-values using {null_method_str}. "
+            f"The input dataset included {self.inputs_['coordinates'].shape[0]} foci from "
+            f"{len(self.inputs_['id'])} experiments."
+        )
+        return description
+
+    def _compute_weights(self, ma_values):
+        """Determine experiment-wise weights per the conventional MKDA approach."""
+        # TODO: Incorporate sample-size and inference metadata extraction and
+        # merging into df.
+        # This will need to be distinct from the kernel_transformer-based kind
+        # done in CBMAEstimator._preprocess_input
+        ids_df = self.inputs_["coordinates"].groupby("id").first()
+
+        n_exp = len(ids_df)
+
+        # Default to unit weighting for missing inference or sample size
+        if "inference" not in ids_df.columns:
+            ids_df["inference"] = "rfx"
+        if "sample_size" not in ids_df.columns:
+            ids_df["sample_size"] = 1.0
+
+        n = ids_df["sample_size"].astype(float).values
+        inf = ids_df["inference"].map({"ffx": 0.75, "rfx": 1.0}).values
+
+        weight_vec = n_exp * ((np.sqrt(n) * inf) / np.sum(np.sqrt(n) * inf))
+        weight_vec = weight_vec[:, None]
+
+        assert weight_vec.shape[0] == ma_values.shape[0]
+        return weight_vec
+
+    def _compute_summarystat_est(self, ma_values):
+        ma_values = ma_values.reshape((ma_values.shape[0], -1))
+        stat_values = ma_values.T.dot(self.weight_vec_)
+
+        if isinstance(ma_values, sparse._coo.core.COO):
+            # NOTE: This may not work correctly with a non-NiftiMasker.
+            mask_data = self.masker.mask_img.get_fdata().astype(bool)
+
+            stat_values = stat_values[mask_data.reshape(-1)].ravel()
+            # This is used by _compute_null_approximate
+            self.__n_mask_voxels = stat_values.shape[0]
+        else:
+            # np.array type is used by _compute_null_reduced_montecarlo
+            stat_values = stat_values.ravel()
+
+        return stat_values
+
+    def _determine_histogram_bins(self, ma_maps):
+        """Determine histogram bins for null distribution methods.
+
+        Parameters
+        ----------
+        ma_maps : :obj:`sparse._coo.core.COO`
+            MA maps.
+            The ma_maps can be a 4d sparse array of MA maps,
+
+        Notes
+        -----
+        This method adds two entries to the null_distributions_ dict attribute: "histogram_bins",
+        and "histogram_means" only if ``null_method == "approximate"``.
+        """
+        if not isinstance(ma_maps, sparse._coo.core.COO):
+            raise ValueError(f"Unsupported data type '{type(ma_maps)}'")
+
+        n_exp = ma_maps.shape[0]
+        prop_active = np.zeros(n_exp)
+        data = ma_maps.data
+        coords = ma_maps.coords
+        for exp_idx in range(n_exp):
+            # The first column of coords is the fourth dimension of the dense array
+            study_ma_values = data[coords[0, :] == exp_idx]
+
+            n_nonzero_voxels = study_ma_values.shape[0]
+            n_zero_voxels = self.__n_mask_voxels - n_nonzero_voxels
+
+            prop_active[exp_idx] = np.mean(np.hstack([study_ma_values, np.zeros(n_zero_voxels)]))
+
+        self.null_distributions_["histogram_bins"] = np.arange(len(prop_active) + 1, step=1)
+
+        if self.null_method.startswith("approximate"):
+            # To speed things up in _compute_null_approximate, we save the means too,
+            self.null_distributions_["histogram_means"] = prop_active
+
+    def _compute_null_approximate(self, ma_maps):
+        """Compute uncorrected null distribution using approximate solution.
+
+        Parameters
+        ----------
+        ma_maps
+            Modeled activation maps. Unused for this estimator.
+
+        Notes
+        -----
+        This method adds one entry to the null_distributions_ dict attribute: "histogram_weights".
+        """
+        assert "histogram_means" in self.null_distributions_.keys()
+
+        # MKDA maps are binary, so we only have k + 1 bins in the final
+        # histogram, where k is the number of studies. We can analytically
+        # compute the null distribution by convolution.
+        # prop_active contains the mean value per experiment
+        prop_active = self.null_distributions_["histogram_means"]
+
+        ss_hist = 1.0
+        for exp_prop in prop_active:
+            ss_hist = np.convolve(ss_hist, [1 - exp_prop, exp_prop])
+
+        self.null_distributions_["histweights_corr-none_method-approximate"] = ss_hist
+
+
+class MKDAChi2(PairwiseCBMAEstimator):
+    r"""Multilevel kernel density analysis- Chi-square analysis.
+
+    The MKDA chi-square method was originally introduced in :footcite:t:`wager2007meta`.
+
+    .. versionchanged:: 0.2.1
+
+        - Make `prior` parameter default to None, which controls if posterior probabilities
+            pFgA, pAgF_prior and pFgA_prior are calculated. This is useful because probability
+            maps are difficult to interpret and for speeding up the algorithm.
+        - Rename ``consistency`` to ``uniformity`` and ``specificity`` to ``association`` to match
+          Neurosynth's terminology
+        - New parameters: ``memory`` and ``memory_level`` for memory caching.
+
+    .. versionchanged:: 0.0.12
+
+        - Use a 4D sparse array for modeled activation maps.
+
+    .. versionchanged:: 0.0.8
+
+        * [REF] Use saved MA maps, when available.
+
+    Parameters
+    ----------
+    kernel_transformer : :obj:`~nimare.meta.kernel.KernelTransformer`, optional
+        Kernel with which to convolve coordinates from dataset. Default is
+        :class:`~nimare.meta.kernel.MKDAKernel`.
+    prior : float, default=0.5
+        Uniform prior probability of each feature being active in a map in
+        the absence of evidence from the map. Default: 0.5
+    memory : instance of :class:`joblib.Memory`, :obj:`str`, or :class:`pathlib.Path`
+        Used to cache the output of a function. By default, no caching is done.
+        If a :obj:`str` is given, it is the path to the caching directory.
+    memory_level : :obj:`int`, default=0
+        Rough estimator of the amount of memory used by caching.
+        Higher value means more memory for caching. Zero means no caching.
+    **kwargs
+        Keyword arguments. Arguments for the kernel_transformer can be assigned
+        here, with the prefix '\kernel__' in the variable name.
+
+    Attributes
+    ----------
+    masker : :class:`~nilearn.input_data.NiftiMasker` or similar
+        Masker object.
+    inputs_ : :obj:`dict`
+        Inputs to the Estimator. For CBMA estimators, there is only one key: coordinates.
+        This is an edited version of the dataset's coordinates DataFrame.
+    null_distributions_ : :obj:`dict` of :class:`numpy.ndarray`
+        Null distributions for any multiple-comparisons correction methods.
+
+        .. important::
+            MKDAChi2 does not retain uncorrected summary-statistic-to-p null distributions,
+            since the summary statistic in this case is the chi-squared value, which has an
+            established null distribution.
+
+        Entries are added to this attribute if and when the corresponding method is applied.
+
+        If :meth:`correct_fwe_montecarlo` is applied:
+
+            -   ``values_desc-pAgF_level-voxel_corr-fwe_method-montecarlo``: The maximum
+                chi-squared value from the p(A|F) one-way chi-squared test from each Monte Carlo
+                iteration. An array of shape (n_iters,).
+            -   ``values_desc-pAgFsize_level-cluster_corr-fwe_method-montecarlo``: The maximum
+                cluster size value from the p(A|F) one-way chi-squared test from each Monte Carlo
+                iteration. An array of shape (n_iters,).
+            -   ``values_desc-pAgFmass_level-cluster_corr-fwe_method-montecarlo``: The maximum
+                cluster mass value from the p(A|F) one-way chi-squared test from each Monte Carlo
+                iteration. An array of shape (n_iters,).
+            -   ``values_desc-pFgA_level-voxel_corr-fwe_method-montecarlo``: The maximum
+                chi-squared value from the p(F|A) two-way chi-squared test from each Monte Carlo
+                iteration. An array of shape (n_iters,).
+            -   ``values_desc-pFgAsize_level-cluster_corr-fwe_method-montecarlo``: The maximum
+                cluster size value from the p(F|A) two-way chi-squared test from each Monte Carlo
+                iteration. An array of shape (n_iters,).
+            -   ``values_desc-pFgAmass_level-cluster_corr-fwe_method-montecarlo``: The maximum
+                cluster mass value from the p(F|A) two-way chi-squared test from each Monte Carlo
+                iteration. An array of shape (n_iters,).
+
+    Notes
+    -----
+    The MKDA Chi-square algorithm was originally implemented as part of the Neurosynth Python
+    library (https://github.com/neurosynth/neurosynth).
+
+    Available correction methods: :meth:`MKDAChi2.correct_fwe_montecarlo`,
+    :meth:`MKDAChi2.correct_fdr_indep`.
+
+    References
+    ----------
+    .. footbibliography::
+    """
+
+    def __init__(
+        self,
+        kernel_transformer=MKDAKernel,
+        prior=0.5,
+        memory=Memory(location=None, verbose=0),
+        memory_level=0,
+        **kwargs,
+    ):
+        if not (isinstance(kernel_transformer, MKDAKernel) or kernel_transformer == MKDAKernel):
+            LGR.warning(
+                f"The KernelTransformer being used ({kernel_transformer}) is not optimized "
+                f"for the {type(self).__name__} algorithm. "
+                "Expect suboptimal performance and beware bugs."
+            )
+
+        # Add kernel transformer attribute and process keyword arguments
+        super().__init__(
+            kernel_transformer=kernel_transformer,
+            memory=memory,
+            memory_level=memory_level,
+            **kwargs,
+        )
+
+        self.prior = prior
+
+    def _generate_description(self):
+        description = (
+            "A multilevel kernel density chi-squared analysis \\citep{wager2007meta} was "
+            "performed according to the same procedure as implemented in Neurosynth with NiMARE "
+            f"{__version__} "
+            "(RRID:SCR_017398; \\citealt{Salo2023}), "
+            f"using a(n) {self.kernel_transformer.__class__.__name__.replace('Kernel', '')} "
+            "kernel. "
+            f"{self.kernel_transformer._generate_description()} "
+            "This analysis calculated several measures. "
+            "The first dataset was evaluated for uniformity of activation via a one-way "
+            "chi-square test. "
+            f"The first input dataset included {self.inputs_['coordinates1'].shape[0]} foci from "
+            f"{len(self.inputs_['id1'])} experiments. "
+            f"The second input dataset included {self.inputs_['coordinates2'].shape[0]} foci from "
+            f"{len(self.inputs_['id2'])} experiments."
+        )
+
+        return description
+
+    def _fit(self, dataset1, dataset2):
+        self.dataset1 = dataset1
+        self.dataset2 = dataset2
+        self.masker = self.masker or dataset1.masker
+        self.null_distributions_ = {}
+
+        # Generate MA maps and calculate count variables for first dataset
+        n_selected_active_voxels = self._collect_ma_maps(
+            maps_key="ma_maps1",
+            coords_key="coordinates1",
+            return_type="summary_array",
+        )
+
+        n_selected = self.dataset1.coordinates["id"].unique().shape[0]
+
+        # Generate MA maps and calculate count variables for second dataset
+        n_unselected_active_voxels = self._collect_ma_maps(
+            maps_key="ma_maps2",
+            coords_key="coordinates2",
+            return_type="summary_array",
+        )
+        n_unselected = self.dataset2.coordinates["id"].unique().shape[0]
+
+        n_mappables = n_selected + n_unselected
+
+        # Nomenclature for variables below: p = probability,
+        # F = feature present, g = given, U = unselected, A = activation.
+        # So, e.g., pAgF = p(A|F) = probability of activation
+        # in a voxel if we know that the feature is present in a study.
+        pF = n_selected / n_mappables
+        pA = np.array(
+            (n_selected_active_voxels + n_unselected_active_voxels) / n_mappables
+        ).squeeze()
+
+        del n_mappables
+
+        pAgF = n_selected_active_voxels / n_selected
+        pAgU = n_unselected_active_voxels / n_unselected
+        pFgA = pAgF * pF / pA
+
+        del pF
+
+        if self.prior:
+            # Recompute conditionals with uniform prior
+            pAgF_prior = self.prior * pAgF + (1 - self.prior) * pAgU
+            pFgA_prior = pAgF * self.prior / pAgF_prior
+
+        # One-way chi-square test for uniformity of activation
+        pAgF_chi2_vals = one_way(np.squeeze(n_selected_active_voxels), n_selected)
+        pAgF_p_vals = chi2.sf(pAgF_chi2_vals, 1)
+        pAgF_sign = np.sign(n_selected_active_voxels - np.mean(n_selected_active_voxels))
+        pAgF_z = p_to_z(pAgF_p_vals, tail="two") * pAgF_sign
+
+        del pAgF_sign
+
+        # Two-way chi-square for association of activation
+        cells = np.squeeze(
+            np.array(
+                [
+                    [n_selected_active_voxels, n_unselected_active_voxels],
+                    [
+                        n_selected - n_selected_active_voxels,
+                        n_unselected - n_unselected_active_voxels,
+                    ],
+                ]
+            ).T
+        )
+
+        del n_selected, n_unselected
+
+        pFgA_chi2_vals = two_way(cells)
+
+        del n_selected_active_voxels, n_unselected_active_voxels
+
+        eps = np.spacing(1)
+        pFgA_p_vals = chi2.sf(pFgA_chi2_vals, 1)
+        pFgA_p_vals[pFgA_p_vals < eps] = eps
+        pFgA_sign = np.sign(pAgF - pAgU).ravel()
+        pFgA_z = p_to_z(pFgA_p_vals, tail="two") * pFgA_sign
+
+        del pFgA_sign, pAgU
+
+        maps = {
+            "z_desc-uniformity": pAgF_z,
+            "z_desc-association": pFgA_z,
+            "chi2_desc-uniformity": pAgF_chi2_vals,
+            "chi2_desc-association": pFgA_chi2_vals,
+            "p_desc-uniformity": pAgF_p_vals,
+            "p_desc-association": pFgA_p_vals,
+            "prob_desc-A": pA,
+            "prob_desc-AgF": pAgF,
+            "prob_desc-FgA": pFgA,
+        }
+
+        if self.prior:
+            maps["prob_desc-AgF_prior"] = pAgF_prior
+            maps["prob_desc-FgA_prior"] = pFgA_prior
+
+        description = self._generate_description()
+        return maps, {}, description
+
+    def _run_fwe_permutation(self, iter_xyz1, iter_xyz2, iter_df1, iter_df2, conn, voxel_thresh):
+        """Run a single permutation of the Monte Carlo FWE correction procedure.
+
+        Parameters
+        ----------
+        iter_xyz1, iter_xyz2 : :obj:`numpy.ndarray`
+            Random coordinates for the permutation.
+        iter_df1, iter_df2 : :obj:`pandas.DataFrame`
+            DataFrames with as many rows as there are coordinates in each of the two datasets,
+            to be filled in with random coordinates for the permutation.
+        conn : :obj:`numpy.ndarray` of shape (3, 3, 3)
+            Connectivity matrix for defining clusters.
+        voxel_thresh : :obj:`float`
+            Uncorrected summary-statistic thresholded for defining clusters.
+
+        Returns
+        -------
+        pAgF_max_chi2_value : :obj:`float`
+            Forward inference maximum chi-squared value, for voxel-level FWE correction.
+        pAgF_max_size : :obj:`float`
+            Forward inference maximum cluster size, for cluster-level FWE correction.
+        pAgF_max_mass : :obj:`float`
+            Forward inference maximum cluster mass, for cluster-level FWE correction.
+        pFgA_max_chi2_value : :obj:`float`
+            Reverse inference maximum chi-squared value, for voxel-level FWE correction.
+        pFgA_max_size : :obj:`float`
+            Reverse inference maximum cluster size, for cluster-level FWE correction.
+        pFgA_max_mass : :obj:`float`
+            Reverse inference maximum cluster mass, for cluster-level FWE correction.
+        """
+        # Not sure if joblib will automatically use a copy of the object, but I'll make a copy to
+        # be safe.
+        iter_df1 = iter_df1.copy()
+        iter_df2 = iter_df2.copy()
+
+        iter_xyz1 = np.squeeze(iter_xyz1)
+        iter_xyz2 = np.squeeze(iter_xyz2)
+        iter_df1[["x", "y", "z"]] = iter_xyz1
+        iter_df2[["x", "y", "z"]] = iter_xyz2
+
+        # Generate MA maps and calculate count variables for first dataset
+        n_selected_active_voxels = self.kernel_transformer.transform(
+            iter_df1, self.masker, return_type="summary_array"
+        )
+
+        n_selected = self.dataset1.coordinates["id"].unique().shape[0]
+
+        # Generate MA maps and calculate count variables for second dataset
+        n_unselected_active_voxels = self.kernel_transformer.transform(
+            iter_df2, self.masker, return_type="summary_array"
+        )
+        n_unselected = self.dataset2.coordinates["id"].unique().shape[0]
+
+        # Currently unused conditional probabilities
+        # pAgF = n_selected_active_voxels / n_selected
+        # pAgU = n_unselected_active_voxels / n_unselected
+
+        # One-way chi-square test for uniformity of activation
+        pAgF_chi2_vals = one_way(np.squeeze(n_selected_active_voxels), n_selected)
+
+        # Voxel-level inference
+        pAgF_max_chi2_value = np.max(np.abs(pAgF_chi2_vals))
+
+        # Cluster-level inference
+        pAgF_chi2_map = self.masker.inverse_transform(pAgF_chi2_vals).get_fdata()
+        pAgF_max_size, pAgF_max_mass = _calculate_cluster_measures(
+            pAgF_chi2_map, voxel_thresh, conn, tail="two"
+        )
+
+        # Two-way chi-square for association of activation
+        cells = np.squeeze(
+            np.array(
+                [
+                    [n_selected_active_voxels, n_unselected_active_voxels],
+                    [
+                        n_selected - n_selected_active_voxels,
+                        n_unselected - n_unselected_active_voxels,
+                    ],
+                ]
+            ).T
+        )
+        pFgA_chi2_vals = two_way(cells)
+
+        # Voxel-level inference
+        pFgA_max_chi2_value = np.max(np.abs(pFgA_chi2_vals))
+
+        # Cluster-level inference
+        pFgA_chi2_map = self.masker.inverse_transform(pFgA_chi2_vals).get_fdata()
+        pFgA_max_size, pFgA_max_mass = _calculate_cluster_measures(
+            pFgA_chi2_map, voxel_thresh, conn, tail="two"
+        )
+
+        return (
+            pAgF_max_chi2_value,
+            pAgF_max_size,
+            pAgF_max_mass,
+            pFgA_max_chi2_value,
+            pFgA_max_size,
+            pFgA_max_mass,
+        )
+
+    def _apply_correction(self, stat_values, voxel_thresh, vfwe_null, csfwe_null, cmfwe_null):
+        """Apply different kinds of FWE correction to statistical value matrix.
+
+        .. versionchanged:: 0.0.13
+
+            Change cluster neighborhood from faces+edges to faces, to match Nilearn.
+
+        Parameters
+        ----------
+        stat_values : :obj:`numpy.ndarray`
+            1D array of summary-statistic values.
+        voxel_thresh : :obj:`float`
+            Summary statistic threshold for defining clusters.
+        vfwe_null, csfwe_null, cmfwe_null : :obj:`numpy.ndarray`
+            Null distributions for FWE correction.
+
+        Returns
+        -------
+        p_vfwe_values, p_csfwe_values, p_cmfwe_values : :obj:`numpy.ndarray`
+            1D arrays of FWE-corrected p-values.
+        """
+        eps = np.spacing(1)
+
+        # Define connectivity matrix for cluster labeling
+        conn = ndimage.generate_binary_structure(rank=3, connectivity=1)
+
+        # Voxel-level FWE
+        p_vfwe_values = null_to_p(np.abs(stat_values), vfwe_null, tail="upper")
+
+        # Crop p-values of 0 or 1 to nearest values that won't evaluate to 0 or 1.
+        # Prevents inf z-values.
+        p_vfwe_values[p_vfwe_values < eps] = eps
+        p_vfwe_values[p_vfwe_values > (1.0 - eps)] = 1.0 - eps
+
+        # Cluster-level FWE
+        # Extract the summary statistics in voxel-wise (3D) form, threshold, and cluster-label
+        stat_map_thresh = self.masker.inverse_transform(stat_values).get_fdata()
+
+        stat_map_thresh[np.abs(stat_map_thresh) <= voxel_thresh] = 0
+
+        # Label positive and negative clusters separately
+        labeled_matrix = np.empty(stat_map_thresh.shape, int)
+        labeled_matrix, _ = ndimage.label(stat_map_thresh > 0, conn)
+        n_positive_clusters = np.max(labeled_matrix)
+        temp_labeled_matrix, _ = ndimage.label(stat_map_thresh < 0, conn)
+        temp_labeled_matrix[temp_labeled_matrix > 0] += n_positive_clusters
+        labeled_matrix = labeled_matrix + temp_labeled_matrix
+        del temp_labeled_matrix
+
+        cluster_labels, idx, cluster_sizes = np.unique(
+            labeled_matrix,
+            return_inverse=True,
+            return_counts=True,
+        )
+        assert cluster_labels[0] == 0
+
+        # Cluster mass-based inference
+        cluster_masses = np.zeros(cluster_labels.shape)
+        for i_val in cluster_labels:
+            if i_val == 0:
+                cluster_masses[i_val] = 0
+
+            cluster_mass = np.sum(np.abs(stat_map_thresh[labeled_matrix == i_val]) - voxel_thresh)
+            cluster_masses[i_val] = cluster_mass
+
+        p_cmfwe_vals = null_to_p(cluster_masses, cmfwe_null, tail="upper")
+        p_cmfwe_map = p_cmfwe_vals[np.reshape(idx, labeled_matrix.shape)]
+
+        p_cmfwe_values = np.squeeze(
+            self.masker.transform(nib.Nifti1Image(p_cmfwe_map, self.masker.mask_img.affine))
+        )
+
+        # Cluster size-based inference
+        cluster_sizes[0] = 0  # replace background's "cluster size" with zeros
+        p_csfwe_vals = null_to_p(cluster_sizes, csfwe_null, tail="upper")
+        p_csfwe_map = p_csfwe_vals[np.reshape(idx, labeled_matrix.shape)]
+        p_csfwe_values = np.squeeze(
+            self.masker.transform(nib.Nifti1Image(p_csfwe_map, self.masker.mask_img.affine))
+        )
+
+        return p_vfwe_values, p_csfwe_values, p_cmfwe_values
+
+    def correct_fwe_montecarlo(self, result, voxel_thresh=0.001, n_iters=1000, n_cores=1):
+        """Perform FWE correction using the max-value permutation method.
+
+        Only call this method from within a Corrector.
+
+        .. versionchanged:: 0.0.13
+
+            Change cluster neighborhood from faces+edges to faces, to match Nilearn.
+
+        .. versionchanged:: 0.0.12
+
+            Include cluster level-corrected results in Monte Carlo null method.
+
+        Parameters
+        ----------
+        result : :obj:`~nimare.results.MetaResult`
+            Result object from a KDA meta-analysis.
+        voxel_thresh : :obj:`float`, default=0.001
+            Voxel-level threshold. Default is 0.001.
+        n_iters : :obj:`int`, default=1000
+            Number of iterations to build the vFWE null distribution.
+            Default is 1000.
+        n_cores : :obj:`int`, default=1
+            Number of cores to use for parallelization.
+            If <=0, defaults to using all available cores. Default is 1.
+
+        Returns
+        -------
+        maps : :obj:`dict`
+            Dictionary of 1D arrays corresponding to masked maps generated by
+            the correction procedure. The following arrays are generated by
+            this method:
+
+            -   ``p_desc-uniformity_level-voxel``: Voxel-level FWE-corrected p-values from the
+                uniformity/forward inference analysis.
+            -   ``z_desc-uniformity_level-voxel``: Voxel-level FWE-corrected z-values from the
+                uniformity/forward inference analysis.
+            -   ``logp_desc-uniformity_level-voxel``: Voxel-level FWE-corrected -log10 p-values
+                from the uniformity/forward inference analysis.
+            -   ``p_desc-uniformityMass_level-cluster``: Cluster-level FWE-corrected p-values
+                from the uniformity/forward inference analysis, using cluster mass.
+            -   ``z_desc-uniformityMass_level-cluster``: Cluster-level FWE-corrected z-values
+                from the uniformity/forward inference analysis, using cluster mass.
+            -   ``logp_desc-uniformityMass_level-cluster``: Cluster-level FWE-corrected -log10
+                p-values from the uniformity/forward inference analysis, using cluster mass.
+            -   ``p_desc-uniformitySize_level-cluster``: Cluster-level FWE-corrected p-values
+                from the uniformity/forward inference analysis, using cluster size.
+            -   ``z_desc-uniformitySize_level-cluster``: Cluster-level FWE-corrected z-values
+                from the uniformity/forward inference analysis, using cluster size.
+            -   ``logp_desc-uniformitySize_level-cluster``: Cluster-level FWE-corrected -log10
+                p-values from the uniformity/forward inference analysis, using cluster size.
+            -   ``p_desc-association_level-voxel``: Voxel-level FWE-corrected p-values from the
+                association/reverse inference analysis.
+            -   ``z_desc-association_level-voxel``: Voxel-level FWE-corrected z-values from the
+                association/reverse inference analysis.
+            -   ``logp_desc-association_level-voxel``: Voxel-level FWE-corrected -log10 p-values
+                from the association/reverse inference analysis.
+            -   ``p_desc-associationMass_level-cluster``: Cluster-level FWE-corrected p-values
+                from the association/reverse inference analysis, using cluster mass.
+            -   ``z_desc-associationMass_level-cluster``: Cluster-level FWE-corrected z-values
+                from the association/reverse inference analysis, using cluster mass.
+            -   ``logp_desc-associationMass_level-cluster``: Cluster-level FWE-corrected -log10
+                p-values from the association/reverse inference analysis, using cluster mass.
+            -   ``p_desc-associationSize_level-cluster``: Cluster-level FWE-corrected p-values
+                from the association/reverse inference analysis, using cluster size.
+            -   ``z_desc-associationSize_level-cluster``: Cluster-level FWE-corrected z-values
+                from the association/reverse inference analysis, using cluster size.
+            -   ``logp_desc-associationSize_level-cluster``: Cluster-level FWE-corrected -log10
+                p-values from the association/reverse inference analysis, using cluster size.
+
+        Notes
+        -----
+        This method adds six new keys to the ``null_distributions_`` attribute:
+
+            -   ``values_desc-pAgF_level-voxel_corr-fwe_method-montecarlo``: The maximum
+                chi-squared value from the p(A|F) one-way chi-squared test from each Monte Carlo
+                iteration. An array of shape (n_iters,).
+            -   ``values_desc-pAgFsize_level-cluster_corr-fwe_method-montecarlo``: The maximum
+                cluster size value from the p(A|F) one-way chi-squared test from each Monte Carlo
+                iteration. An array of shape (n_iters,).
+            -   ``values_desc-pAgFmass_level-cluster_corr-fwe_method-montecarlo``: The maximum
+                cluster mass value from the p(A|F) one-way chi-squared test from each Monte Carlo
+                iteration. An array of shape (n_iters,).
+            -   ``values_desc-pFgA_level-voxel_corr-fwe_method-montecarlo``: The maximum
+                chi-squared value from the p(F|A) two-way chi-squared test from each Monte Carlo
+                iteration. An array of shape (n_iters,).
+            -   ``values_desc-pFgAsize_level-cluster_corr-fwe_method-montecarlo``: The maximum
+                cluster size value from the p(F|A) two-way chi-squared test from each Monte Carlo
+                iteration. An array of shape (n_iters,).
+            -   ``values_desc-pFgAmass_level-cluster_corr-fwe_method-montecarlo``: The maximum
+                cluster mass value from the p(F|A) two-way chi-squared test from each Monte Carlo
+                iteration. An array of shape (n_iters,).
+
+        See Also
+        --------
+        nimare.correct.FWECorrector : The Corrector from which to call this method.
+
+        Examples
+        --------
+        >>> meta = MKDAChi2()
+        >>> result = meta.fit(dset)
+        >>> corrector = FWECorrector(method='montecarlo', n_iters=5, n_cores=1)
+        >>> cresult = corrector.transform(result)
+        """
+        null_xyz = vox2mm(
+            np.vstack(np.where(self.masker.mask_img.get_fdata())).T,
+            self.masker.mask_img.affine,
+        )
+        pAgF_chi2_vals = result.get_map("chi2_desc-uniformity", return_type="array")
+        pFgA_chi2_vals = result.get_map("chi2_desc-association", return_type="array")
+        pAgF_z_vals = result.get_map("z_desc-uniformity", return_type="array")
+        pFgA_z_vals = result.get_map("z_desc-association", return_type="array")
+        pAgF_sign = np.sign(pAgF_z_vals)
+        pFgA_sign = np.sign(pFgA_z_vals)
+
+        n_cores = _check_ncores(n_cores)
+
+        iter_df1 = self.inputs_["coordinates1"]
+        iter_df2 = self.inputs_["coordinates2"]
+        rand_idx1 = np.random.choice(null_xyz.shape[0], size=(iter_df1.shape[0], n_iters))
+        rand_xyz1 = null_xyz[rand_idx1, :]
+        iter_xyzs1 = np.split(rand_xyz1, rand_xyz1.shape[1], axis=1)
+        rand_idx2 = np.random.choice(null_xyz.shape[0], size=(iter_df2.shape[0], n_iters))
+        rand_xyz2 = null_xyz[rand_idx2, :]
+        iter_xyzs2 = np.split(rand_xyz2, rand_xyz2.shape[1], axis=1)
+        eps = np.spacing(1)
+
+        # Identify summary statistic corresponding to intensity threshold
+        ss_thresh = chi2.isf(voxel_thresh, 1)
+
+        # Define connectivity matrix for cluster labeling
+        conn = ndimage.generate_binary_structure(rank=3, connectivity=1)
+
+        perm_results = [
+            r
+            for r in tqdm(
+                Parallel(return_as="generator", n_jobs=n_cores)(
+                    delayed(self._run_fwe_permutation)(
+                        iter_xyz1=iter_xyzs1[i_iter],
+                        iter_xyz2=iter_xyzs2[i_iter],
+                        iter_df1=iter_df1,
+                        iter_df2=iter_df2,
+                        conn=conn,
+                        voxel_thresh=ss_thresh,
+                    )
+                    for i_iter in range(n_iters)
+                ),
+                total=n_iters,
+            )
+        ]
+
+        del rand_idx1, rand_xyz1, iter_xyzs1
+        del rand_idx2, rand_xyz2, iter_xyzs2
+
+        (
+            pAgF_vfwe_null,
+            pAgF_csfwe_null,
+            pAgF_cmfwe_null,
+            pFgA_vfwe_null,
+            pFgA_csfwe_null,
+            pFgA_cmfwe_null,
+        ) = zip(*perm_results)
+
+        del perm_results
+
+        # pAgF_FWE
+        pAgF_p_vfwe_vals, pAgF_p_csfwe_vals, pAgF_p_cmfwe_vals = self._apply_correction(
+            pAgF_chi2_vals,
+            ss_thresh,
+            vfwe_null=pAgF_vfwe_null,
+            csfwe_null=pAgF_csfwe_null,
+            cmfwe_null=pAgF_cmfwe_null,
+        )
+
+        self.null_distributions_["values_desc-pAgF_level-voxel_corr-fwe_method-montecarlo"] = (
+            pAgF_vfwe_null
+        )
+        self.null_distributions_[
+            "values_desc-pAgFsize_level-cluster_corr-fwe_method-montecarlo"
+        ] = pAgF_csfwe_null
+        self.null_distributions_[
+            "values_desc-pAgFmass_level-cluster_corr-fwe_method-montecarlo"
+        ] = pAgF_cmfwe_null
+
+        del pAgF_vfwe_null, pAgF_csfwe_null, pAgF_cmfwe_null
+
+        # pFgA_FWE
+        pFgA_p_vfwe_vals, pFgA_p_csfwe_vals, pFgA_p_cmfwe_vals = self._apply_correction(
+            pFgA_chi2_vals,
+            ss_thresh,
+            vfwe_null=pFgA_vfwe_null,
+            csfwe_null=pFgA_csfwe_null,
+            cmfwe_null=pFgA_cmfwe_null,
+        )
+
+        self.null_distributions_["values_desc-pFgA_level-voxel_corr-fwe_method-montecarlo"] = (
+            pFgA_vfwe_null
+        )
+        self.null_distributions_[
+            "values_desc-pFgAsize_level-cluster_corr-fwe_method-montecarlo"
+        ] = pFgA_csfwe_null
+        self.null_distributions_[
+            "values_desc-pFgAmass_level-cluster_corr-fwe_method-montecarlo"
+        ] = pFgA_cmfwe_null
+
+        del pFgA_vfwe_null, pFgA_csfwe_null, pFgA_cmfwe_null
+
+        # Convert p-values
+        # pAgF
+        pAgF_z_vfwe_vals = p_to_z(pAgF_p_vfwe_vals, tail="two") * pAgF_sign
+        pAgF_logp_vfwe_vals = -np.log10(pAgF_p_vfwe_vals)
+        pAgF_logp_vfwe_vals[np.isinf(pAgF_logp_vfwe_vals)] = -np.log10(eps)
+        pAgF_z_cmfwe_vals = p_to_z(pAgF_p_cmfwe_vals, tail="two") * pAgF_sign
+        pAgF_logp_cmfwe_vals = -np.log10(pAgF_p_cmfwe_vals)
+        pAgF_logp_cmfwe_vals[np.isinf(pAgF_logp_cmfwe_vals)] = -np.log10(eps)
+        pAgF_z_csfwe_vals = p_to_z(pAgF_p_csfwe_vals, tail="two") * pAgF_sign
+        pAgF_logp_csfwe_vals = -np.log10(pAgF_p_csfwe_vals)
+        pAgF_logp_csfwe_vals[np.isinf(pAgF_logp_csfwe_vals)] = -np.log10(eps)
+
+        # pFgA
+        pFgA_z_vfwe_vals = p_to_z(pFgA_p_vfwe_vals, tail="two") * pFgA_sign
+        pFgA_logp_vfwe_vals = -np.log10(pFgA_p_vfwe_vals)
+        pFgA_logp_vfwe_vals[np.isinf(pFgA_logp_vfwe_vals)] = -np.log10(eps)
+        pFgA_z_cmfwe_vals = p_to_z(pFgA_p_cmfwe_vals, tail="two") * pFgA_sign
+        pFgA_logp_cmfwe_vals = -np.log10(pFgA_p_cmfwe_vals)
+        pFgA_logp_cmfwe_vals[np.isinf(pFgA_logp_cmfwe_vals)] = -np.log10(eps)
+        pFgA_z_csfwe_vals = p_to_z(pFgA_p_csfwe_vals, tail="two") * pFgA_sign
+        pFgA_logp_csfwe_vals = -np.log10(pFgA_p_csfwe_vals)
+        pFgA_logp_csfwe_vals[np.isinf(pFgA_logp_csfwe_vals)] = -np.log10(eps)
+
+        maps = {
+            # uniformity analysis
+            "p_desc-uniformity_level-voxel": pAgF_p_vfwe_vals,
+            "z_desc-uniformity_level-voxel": pAgF_z_vfwe_vals,
+            "logp_desc-uniformity_level-voxel": pAgF_logp_vfwe_vals,
+            "p_desc-uniformityMass_level-cluster": pAgF_p_cmfwe_vals,
+            "z_desc-uniformityMass_level-cluster": pAgF_z_cmfwe_vals,
+            "logp_desc-uniformityMass_level-cluster": pAgF_logp_cmfwe_vals,
+            "p_desc-uniformitySize_level-cluster": pAgF_p_csfwe_vals,
+            "z_desc-uniformitySize_level-cluster": pAgF_z_csfwe_vals,
+            "logp_desc-uniformitySize_level-cluster": pAgF_logp_csfwe_vals,
+            # association analysis
+            "p_desc-association_level-voxel": pFgA_p_vfwe_vals,
+            "z_desc-association_level-voxel": pFgA_z_vfwe_vals,
+            "logp_desc-association_level-voxel": pFgA_logp_vfwe_vals,
+            "p_desc-associationMass_level-cluster": pFgA_p_cmfwe_vals,
+            "z_desc-associationMass_level-cluster": pFgA_z_cmfwe_vals,
+            "logp_desc-associationMass_level-cluster": pFgA_logp_cmfwe_vals,
+            "p_desc-associationSize_level-cluster": pFgA_p_csfwe_vals,
+            "z_desc-associationSize_level-cluster": pFgA_z_csfwe_vals,
+            "logp_desc-associationSize_level-cluster": pFgA_logp_csfwe_vals,
+        }
+
+        description = ""
+
+        return maps, {}, description
+
+    def correct_fdr_indep(self, result, alpha=0.05):
+        """Perform FDR correction using the Benjamini-Hochberg method.
+
+        Only call this method from within a Corrector.
+
+        .. versionchanged:: 0.0.12
+
+            Renamed from ``correct_fdr_bh`` to ``correct_fdr_indep``.
+
+        Parameters
+        ----------
+        result : :obj:`~nimare.results.MetaResult`
+            Result object from a KDA meta-analysis.
+        alpha : :obj:`float`, optional
+            Alpha. Default is 0.05.
+
+        Returns
+        -------
+        maps : :obj:`dict`
+            Dictionary of 1D arrays corresponding to masked maps generated by
+            the correction procedure. The following arrays are generated by
+            this method: 'z_desc-uniformity_level-voxel' and 'z_desc-association_level-voxel'.
+
+        See Also
+        --------
+        nimare.correct.FDRCorrector : The Corrector from which to call this method.
+
+        Examples
+        --------
+        >>> meta = MKDAChi2()
+        >>> result = meta.fit(dset)
+        >>> corrector = FDRCorrector(method='indep', alpha=0.05)
+        >>> cresult = corrector.transform(result)
+        """
+        pAgF_p_vals = result.get_map("p_desc-uniformity", return_type="array")
+        pFgA_p_vals = result.get_map("p_desc-association", return_type="array")
+        pAgF_z_vals = result.get_map("z_desc-uniformity", return_type="array")
+        pFgA_z_vals = result.get_map("z_desc-association", return_type="array")
+        pAgF_sign = np.sign(pAgF_z_vals)
+        pFgA_sign = np.sign(pFgA_z_vals)
+        pAgF_p_FDR = fdr(pAgF_p_vals, q=alpha, method="bh")
+        pAgF_z_FDR = p_to_z(pAgF_p_FDR, tail="two") * pAgF_sign
+
+        pFgA_p_FDR = fdr(pFgA_p_vals, q=alpha, method="bh")
+        pFgA_z_FDR = p_to_z(pFgA_p_FDR, tail="two") * pFgA_sign
+
+        maps = {
+            "z_desc-uniformity_level-voxel": pAgF_z_FDR,
+            "z_desc-association_level-voxel": pFgA_z_FDR,
+        }
+
+        description = ""
+
+        return maps, {}, description
+
+
+class KDA(CBMAEstimator):
+    r"""Kernel density analysis.
+
+    .. versionchanged:: 0.2.1
+
+        - New parameters: ``memory`` and ``memory_level`` for memory caching.
+
+    .. versionchanged:: 0.0.12
+
+        - Use a 4D sparse array for modeled activation maps.
+
+    Parameters
+    ----------
+    kernel_transformer : :obj:`~nimare.meta.kernel.KernelTransformer`, optional
+        Kernel with which to convolve coordinates from dataset. Default is
+        :class:`~nimare.meta.kernel.KDAKernel`.
+    null_method : {"approximate", "montecarlo"}, optional
+        Method by which to determine uncorrected p-values. The available options are
+
+        ======================= =================================================================
+        "approximate" (default) Build a histogram of summary-statistic values and their
+                                expected frequencies under the assumption of random spatial
+                                associated between studies, via a weighted convolution.
+
+                                This method is much faster, but slightly less accurate.
+        "montecarlo"            Perform a large number of permutations, in which the coordinates
+                                in the studies are randomly drawn from the Estimator's brain mask
+                                and the full set of resulting summary-statistic values are
+                                incorporated into a null distribution (stored as a histogram for
+                                memory reasons).
+
+                                This method is must slower, and is only slightly more accurate.
+        ======================= =================================================================
+
+    n_iters : int, default=5000
+        Number of iterations to use to define the null distribution.
+        This is only used if ``null_method=="montecarlo"``.
+        Default is 5000.
+    memory : instance of :class:`joblib.Memory`, :obj:`str`, or :class:`pathlib.Path`
+        Used to cache the output of a function. By default, no caching is done.
+        If a :obj:`str` is given, it is the path to the caching directory.
+    memory_level : :obj:`int`, default=0
+        Rough estimator of the amount of memory used by caching.
+        Higher value means more memory for caching. Zero means no caching.
+    n_cores : :obj:`int`, default=1
+        Number of cores to use for parallelization.
+        This is only used if ``null_method=="montecarlo"``.
+        If <=0, defaults to using all available cores.
+        Default is 1.
+    **kwargs
+        Keyword arguments. Arguments for the kernel_transformer can be assigned
+        here, with the prefix '\kernel__' in the variable name.
+
+    Attributes
+    ----------
+    masker : :class:`~nilearn.input_data.NiftiMasker` or similar
+        Masker object.
+    inputs_ : :obj:`dict`
+        Inputs to the Estimator. For CBMA estimators, there is only one key: coordinates.
+        This is an edited version of the dataset's coordinates DataFrame.
+    null_distributions_ : :obj:`dict` of :class:`numpy.ndarray`
+        Null distributions for the uncorrected summary-statistic-to-p-value conversion and any
+        multiple-comparisons correction methods.
+        Entries are added to this attribute if and when the corresponding method is applied.
+
+        If ``null_method == "approximate"``:
+
+            -   ``histogram_bins``: Array of bin centers for the null distribution histogram,
+                ranging from zero to the maximum possible summary statistic value for the Dataset.
+            -   ``histweights_corr-none_method-approximate``: Array of weights for the null
+                distribution histogram, with one value for each bin in ``histogram_bins``.
+
+        If ``null_method == "montecarlo"``:
+
+            -   ``histogram_bins``: Array of bin centers for the null distribution histogram,
+                ranging from zero to the maximum possible summary statistic value for the Dataset.
+            -   ``histweights_corr-none_method-montecarlo``: Array of weights for the null
+                distribution histogram, with one value for each bin in ``histogram_bins``.
+                These values are derived from the full set of summary statistics from each
+                iteration of the Monte Carlo procedure.
+            -   ``histweights_level-voxel_corr-fwe_method-montecarlo``: Array of weights for the
+                voxel-level FWE-correction null distribution, with one value for each bin in
+                ``histogram_bins``. These values are derived from the maximum summary statistic
+                from each iteration of the Monte Carlo procedure.
+
+        If :meth:`correct_fwe_montecarlo` is applied:
+
+            -   ``values_level-voxel_corr-fwe_method-montecarlo``: The maximum summary statistic
+                value from each Monte Carlo iteration. An array of shape (n_iters,).
+            -   ``values_desc-size_level-cluster_corr-fwe_method-montecarlo``: The maximum cluster
+                size from each Monte Carlo iteration. An array of shape (n_iters,).
+            -   ``values_desc-mass_level-cluster_corr-fwe_method-montecarlo``: The maximum cluster
+                mass from each Monte Carlo iteration. An array of shape (n_iters,).
+
+    Notes
+    -----
+    Kernel density analysis was first introduced in :footcite:t:`wager2003valence` and
+    :footcite:t:`wager2004neuroimaging`.
+
+    Available correction methods: :func:`KDA.correct_fwe_montecarlo`
+
+    Warnings
+    --------
+    The KDA algorithm has been replaced in the literature with the MKDA algorithm.
+    As such, this estimator should almost never be used, outside of systematic
+    comparisons between algorithms.
+
+    References
+    ----------
+    .. footbibliography::
+    """
+
+    def __init__(
+        self,
+        kernel_transformer=KDAKernel,
+        null_method="approximate",
+        n_iters=5000,
+        memory=Memory(location=None, verbose=0),
+        memory_level=0,
+        n_cores=1,
+        **kwargs,
+    ):
+        LGR.warning(
+            "The KDA algorithm has been replaced in the literature with the MKDA algorithm. "
+            "As such, this estimator should almost never be used, outside of systematic "
+            "comparisons between algorithms."
+        )
+
+        if not (isinstance(kernel_transformer, KDAKernel) or kernel_transformer == KDAKernel):
+            LGR.warning(
+                f"The KernelTransformer being used ({kernel_transformer}) is not optimized "
+                f"for the {type(self).__name__} algorithm. "
+                "Expect suboptimal performance and beware bugs."
+            )
+
+        # Add kernel transformer attribute and process keyword arguments
+        super().__init__(
+            kernel_transformer=kernel_transformer,
+            memory=memory,
+            memory_level=memory_level,
+            **kwargs,
+        )
+        self.null_method = null_method
+        self.n_iters = None if null_method == "approximate" else n_iters or 5000
+        self.n_cores = _check_ncores(n_cores)
+        self.dataset = None
+
+    def _generate_description(self):
+        """Generate a description of the fitted Estimator.
+
+        Returns
+        -------
+        str
+            Description of the Estimator.
+        """
+        if self.null_method == "montecarlo":
+            null_method_str = (
+                "a Monte Carlo-based null distribution, in which dataset coordinates were "
+                "randomly drawn from the analysis mask and the full set of ALE values were "
+                f"retained, using {self.n_iters} iterations"
+            )
+        else:
+            null_method_str = "an approximate null distribution"
+
+        description = (
+            "A kernel density (KDA) meta-analysis \\citep{wager2007meta} was "
+            "performed was performed with NiMARE "
+            f"{__version__} "
+            "(RRID:SCR_017398; \\citealt{Salo2023}), "
+            f"using a(n) {self.kernel_transformer.__class__.__name__.replace('Kernel', '')} "
+            "kernel. "
+            f"{self.kernel_transformer._generate_description()} "
+            f"Summary statistics (OF values) were converted to p-values using {null_method_str}. "
+            f"The input dataset included {self.inputs_['coordinates'].shape[0]} foci from "
+            f"{len(self.inputs_['id'])} experiments."
+        )
+        return description
+
+    def _compute_summarystat_est(self, ma_values):
+        """Compute OF scores from data.
+
+        Parameters
+        ----------
+        ma_maps : :obj:`numpy.ndarray` or :obj:`sparse._coo.core.COO`
+            MA maps.
+            The ma_maps can be:
+            (1) a 1d contrast-len or 2d contrast-by-voxel array of MA values,
+            or (2) a 4d sparse array of MA maps,
+
+        Returns
+        -------
+        stat_values : 1d array
+            OF values. One value per voxel.
+        """
+        # OF is just a sum of MA values.
+        if isinstance(ma_values, sparse._coo.core.COO):
+            # NOTE: This may not work correctly with a non-NiftiMasker.
+            mask_data = self.masker.mask_img.get_fdata().astype(bool)
+
+            stat_values = ma_values.sum(axis=0)
+
+            stat_values = stat_values.todense().reshape(-1)
+            stat_values = stat_values[mask_data.reshape(-1)]
+
+            # This is used by _compute_null_approximate
+            self.__n_mask_voxels = stat_values.shape[0]
+        else:
+            # np.array type is used by _determine_histogram_bins to calculate max_poss_value
+            stat_values = np.sum(ma_values, axis=0)
+
+        return stat_values
+
+    def _determine_histogram_bins(self, ma_maps):
+        """Determine histogram bins for null distribution methods.
+
+        Parameters
+        ----------
+        ma_maps : :obj:`sparse._coo.core.COO`
+            MA maps.
+
+        Notes
+        -----
+        This method adds one entry to the null_distributions_ dict attribute: "histogram_bins".
+        """
+        if not isinstance(ma_maps, sparse._coo.core.COO):
+            raise ValueError(f"Unsupported data type '{type(ma_maps)}'")
+
+        # assumes that groupby results in same order as MA maps
+        n_foci_per_study = self.inputs_["coordinates"].groupby("id").size().values
+
+        # Determine bins for null distribution histogram
+        if hasattr(self.kernel_transformer, "value"):
+            # Binary-sphere kernels (KDA & MKDA)
+            # The maximum possible MA value for each study is the weighting factor (generally 1)
+            # times the number of foci in the study.
+            # We grab the weighting factor from the kernel transformer.
+            step_size = self.kernel_transformer.value  # typically 1
+            max_ma_values = step_size * n_foci_per_study
+            max_poss_value = self._compute_summarystat_est(max_ma_values)
+        else:
+            # Continuous-sphere kernels (ALE)
+            LGR.info(
+                "A non-binary kernel has been detected. Parameters for the null distribution "
+                "will be guesstimated."
+            )
+
+            N_BINS = 100000
+            # The maximum possible MA value is the max value from each MA map,
+            # unlike the case with a summation-based kernel.
+            # Need to convert to dense because np.ceil is too slow with sparse
+            max_ma_values = ma_maps.max(axis=[1, 2, 3]).todense()
+
+            # round up based on resolution
+            # hardcoding 1000 here because figuring out what to round to was difficult.
+            max_ma_values = np.ceil(max_ma_values * 1000) / 1000
+            max_poss_value = self._compute_summarystat(max_ma_values)
+
+            # create bin centers
+            hist_bins = np.linspace(0, max_poss_value, N_BINS - 1)
+            step_size = hist_bins[1] - hist_bins[0]
+
+        # Weighting is not supported yet, so I'm going to build my bins around the min MA value.
+        # The histogram bins are bin *centers*, not edges.
+        hist_bins = np.arange(0, max_poss_value + (step_size * 1.5), step_size)
+        self.null_distributions_["histogram_bins"] = hist_bins
+
+    def _compute_null_approximate(self, ma_maps):
+        """Compute uncorrected null distribution using approximate solution.
+
+        Parameters
+        ----------
+        ma_maps : :obj:`sparse._coo.core.COO`
+            MA maps.
+
+        Notes
+        -----
+        This method adds two entries to the null_distributions_ dict attribute:
+        "histogram_bins" and "histogram_weights".
+        """
+        if not isinstance(ma_maps, sparse._coo.core.COO):
+            raise ValueError(f"Unsupported data type '{type(ma_maps)}'")
+
+        # Derive bin edges from histogram bin centers for numpy histogram function
+        bin_centers = self.null_distributions_["histogram_bins"]
+        step_size = bin_centers[1] - bin_centers[0]
+        inv_step_size = 1 / step_size
+        bin_edges = bin_centers - (step_size / 2)
+        bin_edges = np.append(bin_centers, bin_centers[-1] + step_size)
+
+        n_exp = ma_maps.shape[0]
+        n_bins = bin_centers.shape[0]
+        ma_hists = np.zeros((n_exp, n_bins))
+        data = ma_maps.data
+        coords = ma_maps.coords
+        for exp_idx in range(n_exp):
+            # The first column of coords is the fourth dimension of the dense array
+            study_ma_values = data[coords[0, :] == exp_idx]
+
+            n_nonzero_voxels = study_ma_values.shape[0]
+            n_zero_voxels = self.__n_mask_voxels - n_nonzero_voxels
+
+            ma_hists[exp_idx, :] = np.histogram(study_ma_values, bins=bin_edges, density=False)[
+                0
+            ].astype(float)
+            ma_hists[exp_idx, 0] += n_zero_voxels
+
+        # Normalize MA histograms to get probabilities
+        ma_hists /= ma_hists.sum(1)[:, None]
+
+        # Null distribution to convert summary statistics to p-values.
+        stat_hist = ma_hists[0, :].copy()
+
+        for i_exp in range(1, ma_hists.shape[0]):
+            exp_hist = ma_hists[i_exp, :]
+
+            # Find histogram bins with nonzero values for each histogram.
+            stat_idx = np.where(stat_hist > 0)[0]
+            exp_idx = np.where(exp_hist > 0)[0]
+
+            # Compute output MA values, stat_hist indices, and probabilities
+            stat_scores = np.add.outer(bin_centers[exp_idx], bin_centers[stat_idx]).ravel()
+            score_idx = np.floor(stat_scores * inv_step_size).astype(int)
+            probabilities = np.outer(exp_hist[exp_idx], stat_hist[stat_idx]).ravel()
+
+            # Reset histogram and set probabilities. Use at() because there can
+            # be redundant values in score_idx.
+            stat_hist = np.zeros(stat_hist.shape)
+            np.add.at(stat_hist, score_idx, probabilities)
+
+        self.null_distributions_["histweights_corr-none_method-approximate"] = stat_hist