From df47483775bfa5c944db6e38e49a3fd38852dfd2 Mon Sep 17 00:00:00 2001 From: JulioAPeraza Date: Thu, 25 Jul 2024 17:45:46 -0700 Subject: [PATCH 1/3] =?UTF-8?q?Add=20Fixed=20Effects=20Meta-Analysis=20wit?= =?UTF-8?q?h=20Hedges=E2=80=99=20g?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- examples/02_meta-analyses/02_plot_ibma.py | 22 +++ nimare/meta/ibma.py | 204 ++++++++++++++++++---- nimare/resources/references.bib | 10 ++ nimare/tests/test_meta_ibma.py | 8 + nimare/transforms.py | 45 +++++ 5 files changed, 258 insertions(+), 31 deletions(-) diff --git a/examples/02_meta-analyses/02_plot_ibma.py b/examples/02_meta-analyses/02_plot_ibma.py index 6d0d4458d..b04d6dfff 100644 --- a/examples/02_meta-analyses/02_plot_ibma.py +++ b/examples/02_meta-analyses/02_plot_ibma.py @@ -200,3 +200,25 @@ pprint(results.description_) print("References:") pprint(results.bibtex_) + + +############################################################################### +# Fixed Effects Meta-Analysis with Hedges’ g +# ----------------------------------------------------------------------------- +from nimare.meta.ibma import FixedEffectsHedges + +meta = FixedEffectsHedges(tau2=0) +results = meta.fit(dset) + +plot_stat_map( + results.get_map("z"), + cut_coords=[0, 0, -8], + draw_cross=False, + cmap="RdBu_r", + symmetric_cbar=True, +) + +print("Description:") +pprint(results.description_) +print("References:") +pprint(results.bibtex_) diff --git a/nimare/meta/ibma.py b/nimare/meta/ibma.py index 8329e30e9..e9a3eeef3 100755 --- a/nimare/meta/ibma.py +++ b/nimare/meta/ibma.py @@ -25,7 +25,7 @@ from nimare import _version from nimare.estimator import Estimator from nimare.meta.utils import _apply_liberal_mask -from nimare.transforms import p_to_z, t_to_z +from nimare.transforms import p_to_z, t_to_z, t_to_d, d_to_g from nimare.utils import _boolean_unmask, _check_ncores, get_masker LGR = logging.getLogger(__name__) @@ -168,8 +168,8 @@ class Fishers(IBMAEstimator): .. versionchanged:: 0.3.0 * New parameter: ``two_sided``, controls the type of test to be performed. In addition, - the default is now set to True (two-sided), which differs from previous versions - where only one-sided tests were performed. + the default is now set to True (two-sided), which differs from previous versions + where only one-sided tests were performed. .. versionchanged:: 0.2.1 @@ -299,11 +299,11 @@ class Stouffers(IBMAEstimator): .. versionchanged:: 0.3.0 * New parameter: ``two_sided``, controls the type of test to be performed. In addition, - the default is now set to True (two-sided), which differs from previous versions - where only one-sided tests were performed. + the default is now set to True (two-sided), which differs from previous versions + where only one-sided tests were performed. * Add correction for multiple contrasts within a study. * New parameter: ``normalize_contrast_weights`` to normalized the weights by the - number of contrasts in each study. + number of contrasts in each study. .. versionchanged:: 0.2.1 @@ -625,10 +625,8 @@ def _fit(self, dataset): ) else: n_voxels = self.inputs_["beta_maps"].shape[1] - z_map = np.zeros(n_voxels, dtype=float) - p_map = np.zeros(n_voxels, dtype=float) - est_map = np.zeros(n_voxels, dtype=float) - se_map = np.zeros(n_voxels, dtype=float) + + z_map, p_map, est_map, se_map = [np.zeros(n_voxels, dtype=float) for _ in range(4)] dof_map = np.zeros(n_voxels, dtype=np.int32) beta_bags = self.inputs_["data_bags"]["beta_maps"] @@ -770,11 +768,10 @@ def _fit(self, dataset): ) else: n_voxels = self.inputs_["beta_maps"].shape[1] - z_map = np.zeros(n_voxels, dtype=float) - p_map = np.zeros(n_voxels, dtype=float) - est_map = np.zeros(n_voxels, dtype=float) - se_map = np.zeros(n_voxels, dtype=float) - tau2_map = np.zeros(n_voxels, dtype=float) + + z_map, p_map, est_map, se_map, tau2_map = [ + np.zeros(n_voxels, dtype=float) for _ in range(5) + ] dof_map = np.zeros(n_voxels, dtype=np.int32) beta_bags = self.inputs_["data_bags"]["beta_maps"] @@ -921,11 +918,10 @@ def _fit(self, dataset): ) else: n_voxels = self.inputs_["beta_maps"].shape[1] - z_map = np.zeros(n_voxels, dtype=float) - p_map = np.zeros(n_voxels, dtype=float) - est_map = np.zeros(n_voxels, dtype=float) - se_map = np.zeros(n_voxels, dtype=float) - tau2_map = np.zeros(n_voxels, dtype=float) + + z_map, p_map, est_map, se_map, tau2_map = [ + np.zeros(n_voxels, dtype=float) for _ in range(5) + ] dof_map = np.zeros(n_voxels, dtype=np.int32) beta_bags = self.inputs_["data_bags"]["beta_maps"] @@ -1090,12 +1086,10 @@ def _fit(self, dataset): ) else: n_voxels = self.inputs_["beta_maps"].shape[1] - z_map = np.zeros(n_voxels, dtype=float) - p_map = np.zeros(n_voxels, dtype=float) - est_map = np.zeros(n_voxels, dtype=float) - se_map = np.zeros(n_voxels, dtype=float) - tau2_map = np.zeros(n_voxels, dtype=float) - sigma2_map = np.zeros(n_voxels, dtype=float) + + z_map, p_map, est_map, se_map, tau2_map, sigma2_map = [ + np.zeros(n_voxels, dtype=float) for _ in range(6) + ] dof_map = np.zeros(n_voxels, dtype=np.int32) for bag in self.inputs_["data_bags"]["beta_maps"]: @@ -1263,11 +1257,10 @@ def _fit(self, dataset): ) else: n_voxels = self.inputs_["beta_maps"].shape[1] - z_map = np.zeros(n_voxels, dtype=float) - p_map = np.zeros(n_voxels, dtype=float) - est_map = np.zeros(n_voxels, dtype=float) - se_map = np.zeros(n_voxels, dtype=float) - tau2_map = np.zeros(n_voxels, dtype=float) + + z_map, p_map, est_map, se_map, tau2_map = [ + np.zeros(n_voxels, dtype=float) for _ in range(5) + ] dof_map = np.zeros(n_voxels, dtype=np.int32) beta_bags = self.inputs_["data_bags"]["beta_maps"] @@ -1525,3 +1518,152 @@ def correct_fwe_montecarlo(self, result, n_iters=5000, n_cores=1): ) return maps, {}, description + + +class FixedEffectsHedges(IBMAEstimator): + """Fixed Effects Hedges meta-regression estimator + + .. versionadded:: 0.3.1 + + Provides the weighted least-squares estimate of the fixed effects using Hedge's g + as the point estimate and the variance of bias-corrected Cohen's d as the variance + estimate, and given known/assumed between-study variance tau^2. + When tau^2 = 0 (default), the model is the standard inverse-weighted + fixed-effects meta-regression. + + This method was described in :footcite:t:`bossier2019`. + + Parameters + ---------- + aggressive_mask : :obj:`bool`, optional + Voxels with a value of zero of NaN in any of the input maps will be removed + from the analysis. + If False, all voxels are included by running a separate analysis on bags + of voxels that belong that have a valid value across the same studies. + Default is True. + tau2 : :obj:`float` or 1D :class:`numpy.ndarray`, optional + Assumed/known value of tau^2. Must be >= 0. Default is 0. + + Notes + ----- + Requires `t` images and sample size from metadata. + + :meth:`fit` produces a :class:`~nimare.results.MetaResult` object with the following maps: + + ============== =============================================================================== + "z" Z-statistic map from one-sample test. + "p" P-value map from one-sample test. + "est" Fixed effects estimate for intercept test. + "se" Standard error of fixed effects estimate. + "dof" Degrees of freedom map from one-sample test. + ============== =============================================================================== + + Warnings + -------- + Masking approaches which average across voxels (e.g., NiftiLabelsMaskers) + will likely result in biased results. The extent of this bias is currently + unknown. + + By default, all image-based meta-analysis estimators adopt an aggressive masking + strategy, in which any voxels with a value of zero in any of the input maps + will be removed from the analysis. Setting ``aggressive_mask=False`` will + instead run tha analysis in bags of voxels that have a valid value across + the same studies. + + References + ---------- + .. footbibliography:: + + See Also + -------- + :class:`pymare.estimators.WeightedLeastSquares`: + The PyMARE estimator called by this class. + """ + + _required_inputs = {"t_maps": ("image", "t"), "sample_sizes": ("metadata", "sample_sizes")} + + def __init__(self, tau2=0, **kwargs): + super().__init__(**kwargs) + self.tau2 = tau2 + + def _generate_description(self): + description = ( + f"An image-based meta-analysis was performed with NiMARE {__version__} " + "(RRID:SCR_017398; \\citealt{Salo2023}), on " + f"{len(self.inputs_['id'])} t-statistic images using Heges' g as point estimates " + "and the variance of bias-corrected Cohen's in a Weighted Least Squares approach " + "\\citep{brockwell2001comparison,bossier2019}, " + f"with an a priori tau-squared value of {self.tau2} defined across all voxels." + ) + return description + + def _fit_model(self, t_maps, study_mask=None): + """Fit the model to the data.""" + n_studies, n_voxels = t_maps.shape + + if study_mask is None: + # If no mask is provided, assume all studies are included. This is always the case + # when using the aggressive mask. + study_mask = np.arange(n_studies) + + sample_sizes = np.array([np.mean(self.inputs_["sample_sizes"][idx]) for idx in study_mask]) + n_maps = np.tile(sample_sizes, (n_voxels, 1)).T + + # Calculate Hedge's g maps: Standardized mean + cohens_maps = t_to_d(t_maps, n_maps) + hedges_maps, var_hedges_maps = d_to_g(cohens_maps, n_maps, return_variance=True) + + del n_maps, sample_sizes, cohens_maps + + pymare_dset = pymare.Dataset(y=hedges_maps, v=var_hedges_maps) + est = pymare.estimators.WeightedLeastSquares(tau2=self.tau2) + est.fit_dataset(pymare_dset) + est_summary = est.summary() + + fe_stats = est_summary.get_fe_stats() + z_map = fe_stats["z"].squeeze() + p_map = fe_stats["p"].squeeze() + est_map = fe_stats["est"].squeeze() + se_map = fe_stats["se"].squeeze() + dof_map = np.tile(n_studies - 1, n_voxels).astype(np.int32) + + return z_map, p_map, est_map, se_map, dof_map + + def _fit(self, dataset): + self.dataset = dataset + self.masker = self.masker or dataset.masker + if not isinstance(self.masker, NiftiMasker): + LGR.warning( + f"A {type(self.masker)} mask has been detected. " + "Masks which average across voxels will likely produce biased results when used " + "with this Estimator." + ) + + if self.aggressive_mask: + voxel_mask = self.inputs_["aggressive_mask"] + result_maps = self._fit_model(self.inputs_["t_maps"][:, voxel_mask]) + + z_map, p_map, est_map, se_map, dof_map = tuple( + map(lambda x: _boolean_unmask(x, voxel_mask), result_maps) + ) + else: + n_voxels = self.inputs_["t_maps"].shape[1] + + z_map, p_map, est_map, se_map = [np.zeros(n_voxels, dtype=float) for _ in range(4)] + dof_map = np.zeros(n_voxels, dtype=np.int32) + + for bag in self.inputs_["data_bags"]["t_maps"]: + ( + z_map[bag["voxel_mask"]], + p_map[bag["voxel_mask"]], + est_map[bag["voxel_mask"]], + se_map[bag["voxel_mask"]], + dof_map[bag["voxel_mask"]], + ) = self._fit_model(bag["values"], bag["study_mask"]) + + # tau2 is a float, not a map, so it can't go into the results dictionary + tables = {"level-estimator": pd.DataFrame(columns=["tau2"], data=[self.tau2])} + maps = {"z": z_map, "p": p_map, "est": est_map, "se": se_map, "dof": dof_map} + description = self._generate_description() + + return maps, tables, description diff --git a/nimare/resources/references.bib b/nimare/resources/references.bib index 263db3dd5..04e9eb9ab 100644 --- a/nimare/resources/references.bib +++ b/nimare/resources/references.bib @@ -529,3 +529,13 @@ @article{geoffroy2001poisson year={2001}, publisher={Taylor \& Francis} } + +@article {bossier2019, + author = {Bossier, Han and Nichols, Thomas E. and Moerkerke, Beatrijs}, + title = {Standardized Effect Sizes and Image-Based Meta-Analytical Approaches for fMRI Data}, + elocation-id = {865881}, + year = {2019}, + doi = {10.1101/865881}, + publisher = {Cold Spring Harbor Laboratory}, + journal = {bioRxiv} +} diff --git a/nimare/tests/test_meta_ibma.py b/nimare/tests/test_meta_ibma.py index 8f41d630a..e1e4f87dc 100644 --- a/nimare/tests/test_meta_ibma.py +++ b/nimare/tests/test_meta_ibma.py @@ -120,6 +120,14 @@ ("t", "z", "dof"), id="PermutedOLS", ), + pytest.param( + ibma.FixedEffectsHedges, + {"tau2": 0}, + None, + {}, + ("z", "p", "est", "se", "dof"), + id="FixedEffectsHedges", + ), ], ) @pytest.mark.parametrize("aggressive_mask", [True, False], ids=["aggressive", "liberal"]) diff --git a/nimare/transforms.py b/nimare/transforms.py index 40d536cdd..64aeb4fe2 100644 --- a/nimare/transforms.py +++ b/nimare/transforms.py @@ -860,3 +860,48 @@ def z_to_t(z_values, dof): t_values = np.zeros(z_values.shape) t_values[z_values != 0] = t_values_nonzero return t_values + + +def t_to_d(t_values, sample_sizes): + """Convert t-statistics to Cohen's d. + + Parameters + ---------- + t_values : array_like + T-statistics + sample_sizes : array_like + Sample sizes + + Returns + ------- + d_values : array_like + Cohen's d + """ + d_values = t_values / np.sqrt(sample_sizes) + return d_values + + +def d_to_g(d, N, return_variance=False): + """Convert Cohen's d to Hedges' g. + + Parameters + ---------- + d : array_like + Cohen's d + N : array_like + Sample sizes + return_variance : bool, optional + Whether to return the variance of Hedges' g. Default is False. + + Returns + ------- + g_values : array_like + Hedges' g + """ + # Calculate bias correction h(N) + h = 1 - (3 / (4 * (N - 1) - 1)) + + if return_variance: + return d * h, ((N - 1) * (1 + N * d**2) * (h**2) / (N * (N - 3))) - d**2 + + return d * h From 525908b6b8f78f8887939e26fbc1fe28884b1f85 Mon Sep 17 00:00:00 2001 From: JulioAPeraza Date: Thu, 25 Jul 2024 17:58:40 -0700 Subject: [PATCH 2/3] Fix style check error --- nimare/meta/ibma.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nimare/meta/ibma.py b/nimare/meta/ibma.py index e9a3eeef3..5e6e01df6 100755 --- a/nimare/meta/ibma.py +++ b/nimare/meta/ibma.py @@ -25,7 +25,7 @@ from nimare import _version from nimare.estimator import Estimator from nimare.meta.utils import _apply_liberal_mask -from nimare.transforms import p_to_z, t_to_z, t_to_d, d_to_g +from nimare.transforms import d_to_g, p_to_z, t_to_d, t_to_z from nimare.utils import _boolean_unmask, _check_ncores, get_masker LGR = logging.getLogger(__name__) From 080169e108b332624a2c93bd7866484847b1653c Mon Sep 17 00:00:00 2001 From: JulioAPeraza Date: Thu, 25 Jul 2024 18:31:00 -0700 Subject: [PATCH 3/3] Fix style check --- nimare/meta/ibma.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nimare/meta/ibma.py b/nimare/meta/ibma.py index 5e6e01df6..4bac501e6 100755 --- a/nimare/meta/ibma.py +++ b/nimare/meta/ibma.py @@ -1521,7 +1521,7 @@ def correct_fwe_montecarlo(self, result, n_iters=5000, n_cores=1): class FixedEffectsHedges(IBMAEstimator): - """Fixed Effects Hedges meta-regression estimator + """Fixed Effects Hedges meta-regression estimator. .. versionadded:: 0.3.1