neurosynth/analysis/meta.py
def analyze_features(dataset, features=None, image_type='association-test_z',
                     threshold=0.001, q=0.01, output_dir=None, prefix=None):
    """ Generate meta-analysis images for a set of features.
    Args:
        dataset: A Dataset instance containing feature and activation data.
        features: A list of named features to generate meta-analysis maps for.
            If None, analyzes all features in the current dataset.
        image_type: The type of image to return. Specify one of the extensions
            generated by the MetaAnalysis procedure--e.g., association-test_z,
            uniformity-test_z, etc.  By default, will use
            association-test_z (i.e., z-scores reflecting the association
            between presence of activation and presence of feature).
        threshold: The threshold for determining whether or not a Mappable has
            a feature. By default, this is 0.001, which is only sensible in the
            case of term-based features (so be sure to specify it for other
            kinds).
        q: The FDR rate to use for multiple comparisons correction (default =
            0.05).
        output_dir: Directory to save all meta-analysis images to. If none,
            returns all the data as a matrix.
        prefix: All output images will be prepended with this string (if None,
            defaults to the name of the feature).
    Returns:
        If output_dir is None, an n_voxels x n_features 2D numpy array.
    """
    if features is None:
        features = dataset.get_feature_names()
    if output_dir is None:
        result = np.zeros((dataset.masker.n_vox_in_mask, len(features)))

    for i, f in enumerate(features):
        ids = dataset.get_studies(features=f, frequency_threshold=threshold)
        ma = MetaAnalysis(dataset, ids, q=q)
        if output_dir is None:
            result[:, i] = ma.images[image_type]
        else:
            pfx = f if prefix is None else prefix + '_' + f
            ma.save_results(output_dir=output_dir, prefix=pfx)

    if output_dir is None:
        return result
def analyze_features(dataset, features=None, image_type='association-test_z',
                     threshold=0.001, q=0.01, output_dir=None, prefix=None):
    """ Generate meta-analysis images for a set of features.
    Args:
        dataset: A Dataset instance containing feature and activation data.
        features: A list of named features to generate meta-analysis maps for.
            If None, analyzes all features in the current dataset.
        image_type: The type of image to return. Specify one of the extensions
            generated by the MetaAnalysis procedure--e.g., association-test_z,
            uniformity-test_z, etc.  By default, will use
            association-test_z (i.e., z-scores reflecting the association
            between presence of activation and presence of feature).
        threshold: The threshold for determining whether or not a Mappable has
            a feature. By default, this is 0.001, which is only sensible in the
            case of term-based features (so be sure to specify it for other
            kinds).
        q: The FDR rate to use for multiple comparisons correction (default =
            0.05).
        output_dir: Directory to save all meta-analysis images to. If none,
            returns all the data as a matrix.
        prefix: All output images will be prepended with this string (if None,
            defaults to the name of the feature).
    Returns:
        If output_dir is None, an n_voxels x n_features 2D numpy array.
    """
    if features is None:
        features = dataset.get_feature_names()
    if output_dir is None:
        result = np.zeros((dataset.masker.n_vox_in_mask, len(features)))

    for i, f in enumerate(features):
        ids = dataset.get_studies(features=f, frequency_threshold=threshold)
        ma = MetaAnalysis(dataset, ids, q=q)
        if output_dir is None:
            result[:, i] = ma.images[image_type]
        else:
            pfx = f if prefix is None else prefix + '_' + f
            ma.save_results(output_dir=output_dir, prefix=pfx)

    if output_dir is None:
        return result
def analyze_features ( dataset , features = None , image_type = 'association-test_z' , threshold = 0.001 , q = 0.01 , output_dir = None , prefix = None ) : if features is None : features = dataset . get_feature_names ( ) if output_dir is None : result = np . zeros ( ( dataset . masker . n_vox_in_mask , len ( features ) ) ) for i , f in enumerate ( features ) : ids = dataset . get_studies ( features = f , frequency_threshold = threshold ) ma = MetaAnalysis ( dataset , ids , q = q ) if output_dir is None : result [ : , i ] = ma . images [ image_type ] else : pfx = f if prefix is None else prefix + '_' + f ma . save_results ( output_dir = output_dir , prefix = pfx ) if output_dir is None : return result
Generate meta-analysis images for a set of features.
    Args:
        dataset: A Dataset instance containing feature and activation data.
        features: A list of named features to generate meta-analysis maps for.
            If None, analyzes all features in the current dataset.
        image_type: The type of image to return. Specify one of the extensions
            generated by the MetaAnalysis procedure--e.g., association-test_z,
            uniformity-test_z, etc.  By default, will use
            association-test_z (i.e., z-scores reflecting the association
            between presence of activation and presence of feature).
        threshold: The threshold for determining whether or not a Mappable has
            a feature. By default, this is 0.001, which is only sensible in the
            case of term-based features (so be sure to specify it for other
            kinds).
        q: The FDR rate to use for multiple comparisons correction (default =
            0.05).
        output_dir: Directory to save all meta-analysis images to. If none,
            returns all the data as a matrix.
        prefix: All output images will be prepended with this string (if None,
            defaults to the name of the feature).
    Returns:
        If output_dir is None, an n_voxels x n_features 2D numpy array.
Generate meta - analysis images for a set of features . Args : dataset : A Dataset instance containing feature and activation data . features : A list of named features to generate meta - analysis maps for . If None analyzes all features in the current dataset . image_type : The type of image to return . Specify one of the extensions generated by the MetaAnalysis procedure -- e . g . association - test_z uniformity - test_z etc . By default will use association - test_z ( i . e . z - scores reflecting the association between presence of activation and presence of feature ) . threshold : The threshold for determining whether or not a Mappable has a feature . By default this is 0 . 001 which is only sensible in the case of term - based features ( so be sure to specify it for other kinds ) . q : The FDR rate to use for multiple comparisons correction ( default = 0 . 05 ) . output_dir : Directory to save all meta - analysis images to . If none returns all the data as a matrix . prefix : All output images will be prepended with this string ( if None defaults to the name of the feature ) . Returns : If output_dir is None an n_voxels x n_features 2D numpy array .