def _fit(self, dataset):
self.dataset = dataset
# Use intercept as explanatory variable
self.parameters_["tested_vars"] = np.ones(
(self.inputs_["z_maps"].shape[0], 1))
self.parameters_["confounding_vars"] = None
_, t_map, _ = permuted_ols(
self.parameters_["tested_vars"],
self.inputs_["z_maps"],
confounding_vars=self.parameters_["confounding_vars"],
model_intercept=False, # modeled by tested_vars
n_perm=0,
two_sided_test=self.two_sided,
random_state=42,
n_jobs=1,
verbose=0,
)
# Convert t to z, preserving signs
dof = self.parameters_["tested_vars"].shape[0] - self.parameters_[
"tested_vars"].shape[1]
z_map = t_to_z(t_map, dof)
images = {
"t": _boolean_unmask(t_map.squeeze(),
self.inputs_["aggressive_mask"]),
"z": _boolean_unmask(z_map.squeeze(),
self.inputs_["aggressive_mask"]),
}
return images
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.")
est = pymare.estimators.VarianceBasedLikelihoodEstimator(
method=self.method)
pymare_dset = pymare.Dataset(y=self.inputs_["beta_maps"],
v=self.inputs_["varcope_maps"])
est.fit_dataset(pymare_dset)
est_summary = est.summary()
results = {
"tau2":
_boolean_unmask(est_summary.tau2.squeeze(),
self.inputs_["aggressive_mask"]),
"z":
_boolean_unmask(est_summary.get_fe_stats()["z"].squeeze(),
self.inputs_["aggressive_mask"]),
"p":
_boolean_unmask(est_summary.get_fe_stats()["p"].squeeze(),
self.inputs_["aggressive_mask"]),
"est":
_boolean_unmask(est_summary.get_fe_stats()["est"].squeeze(),
self.inputs_["aggressive_mask"]),
}
return results
def _fit(self, dataset):
self.dataset = dataset
self.masker = self.masker or dataset.masker
sample_sizes = np.array(
[np.mean(n) for n in self.inputs_["sample_sizes"]])
n_maps = np.tile(sample_sizes,
(self.inputs_["beta_maps"].shape[1], 1)).T
pymare_dset = pymare.Dataset(y=self.inputs_["beta_maps"], n=n_maps)
est = pymare.estimators.SampleSizeBasedLikelihoodEstimator(
method=self.method)
est.fit_dataset(pymare_dset)
est_summary = est.summary()
results = {
"tau2":
_boolean_unmask(est_summary.tau2.squeeze(),
self.inputs_["aggressive_mask"]),
"z":
_boolean_unmask(est_summary.get_fe_stats()["z"].squeeze(),
self.inputs_["aggressive_mask"]),
"p":
_boolean_unmask(est_summary.get_fe_stats()["p"].squeeze(),
self.inputs_["aggressive_mask"]),
"est":
_boolean_unmask(est_summary.get_fe_stats()["est"].squeeze(),
self.inputs_["aggressive_mask"]),
}
return results
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.")
pymare_dset = pymare.Dataset(y=self.inputs_["beta_maps"],
v=self.inputs_["varcope_maps"])
est = pymare.estimators.WeightedLeastSquares(tau2=self.tau2)
est.fit_dataset(pymare_dset)
est_summary = est.summary()
# tau2 is an float, not a map, so it can't go in the results dictionary
results = {
"z":
_boolean_unmask(est_summary.get_fe_stats()["z"].squeeze(),
self.inputs_["aggressive_mask"]),
"p":
_boolean_unmask(est_summary.get_fe_stats()["p"].squeeze(),
self.inputs_["aggressive_mask"]),
"est":
_boolean_unmask(est_summary.get_fe_stats()["est"].squeeze(),
self.inputs_["aggressive_mask"]),
}
return results
def _fit(self, dataset):
self.dataset = dataset
self.masker = self.masker or dataset.masker
if not isinstance(self.masker, NiftiMasker):
raise ValueError(
f"A {type(self.masker)} mask has been detected. "
"Only NiftiMaskers are allowed for this Estimator. "
"This is because aggregation, such as averaging values across ROIs, "
"will produce invalid results.")
est = pymare.estimators.StoufferCombinationTest()
if self.use_sample_size:
sample_sizes = np.array(
[np.mean(n) for n in self.inputs_["sample_sizes"]])
weights = np.sqrt(sample_sizes)
weight_maps = np.tile(weights,
(self.inputs_["z_maps"].shape[1], 1)).T
pymare_dset = pymare.Dataset(y=self.inputs_["z_maps"],
v=weight_maps)
else:
pymare_dset = pymare.Dataset(y=self.inputs_["z_maps"])
est.fit_dataset(pymare_dset)
est_summary = est.summary()
results = {
"z":
_boolean_unmask(est_summary.z.squeeze(),
self.inputs_["aggressive_mask"]),
"p":
_boolean_unmask(est_summary.p.squeeze(),
self.inputs_["aggressive_mask"]),
}
return results
def _fit(self, dataset):
self.dataset = dataset
self.masker = self.masker or dataset.masker
if not isinstance(self.masker, NiftiMasker):
raise ValueError(
f"A {type(self.masker)} mask has been detected. "
"Only NiftiMaskers are allowed for this Estimator. "
"This is because aggregation, such as averaging values across ROIs, "
"will produce invalid results.")
pymare_dset = pymare.Dataset(y=self.inputs_["z_maps"])
est = pymare.estimators.FisherCombinationTest()
est.fit_dataset(pymare_dset)
est_summary = est.summary()
results = {
"z":
_boolean_unmask(est_summary.z.squeeze(),
self.inputs_["aggressive_mask"]),
"p":
_boolean_unmask(est_summary.p.squeeze(),
self.inputs_["aggressive_mask"]),
}
return results
def correct_fwe_montecarlo(self, result, n_iters=10000, n_cores=1):
"""Perform FWE correction using the max-value permutation method.
.. versionchanged:: 0.0.8
* [FIX] Remove single-dimensional entries of each array of returns (:obj:`dict`).
.. versionadded:: 0.0.4
Only call this method from within a Corrector.
Parameters
----------
result : :obj:`~nimare.results.MetaResult`
Result object from an ALE meta-analysis.
n_iters : :obj:`int`, optional
The number of iterations to run in estimating the null distribution.
Default is 10000.
n_cores : :obj:`int`, optional
Number of cores to use for parallelization.
If <=0, defaults to using all available cores. Default is 1.
Returns
-------
images : :obj:`dict`
Dictionary of 1D arrays corresponding to masked images generated by
the correction procedure. The following arrays are generated by
this method: 'z_vthresh', 'p_level-voxel', 'z_level-voxel', and
'logp_level-cluster'.
See Also
--------
nimare.correct.FWECorrector : The Corrector from which to call this method.
nilearn.mass_univariate.permuted_ols : The function used for this IBMA.
Examples
--------
>>> meta = PermutedOLS()
>>> result = meta.fit(dset)
>>> corrector = FWECorrector(method='montecarlo',
n_iters=5, n_cores=1)
>>> cresult = corrector.transform(result)
"""
n_cores = _check_ncores(n_cores)
log_p_map, t_map, _ = permuted_ols(
self.parameters_["tested_vars"],
self.inputs_["z_maps"],
confounding_vars=self.parameters_["confounding_vars"],
model_intercept=False, # modeled by tested_vars
n_perm=n_iters,
two_sided_test=self.two_sided,
random_state=42,
n_jobs=n_cores,
verbose=0,
)
# Fill complete maps
p_map = np.power(10.0, -log_p_map)
# Convert p to z, preserving signs
sign = np.sign(t_map)
sign[sign == 0] = 1
z_map = p_to_z(p_map, tail="two") * sign
images = {
"logp_level-voxel":
_boolean_unmask(log_p_map.squeeze(),
self.inputs_["aggressive_mask"]),
"z_level-voxel":
_boolean_unmask(z_map.squeeze(), self.inputs_["aggressive_mask"]),
}
return images