Note

This page is a reference documentation. It only explains the class signature, and not how to use it. Please refer to the user guide for the big picture.

8.1.1. nilearn.connectome.ConnectivityMeasure

class nilearn.connectome.ConnectivityMeasure(cov_estimator=LedoitWolf(store_precision=False), kind='covariance', vectorize=False, discard_diagonal=False)

A class that computes different kinds of functional connectivity matrices.

New in version 0.2.

Parameters:

cov_estimator : estimator object, optional.

The covariance estimator. By default the LedoitWolf estimator is used. This implies that correlations are slightly shrunk towards zero compared to a maximum-likelihood estimate

kind : {“correlation”, “partial correlation”, “tangent”, “covariance”, “precision”}, optional

The matrix kind.

vectorize : bool, optional

If True, connectivity matrices are reshaped into 1D arrays and only their flattened lower triangular parts are returned.

discard_diagonal : bool, optional

If True, vectorized connectivity coefficients do not include the matrices diagonal elements. Used only when vectorize is set to True.

References

For the use of “tangent”, see the paper: G. Varoquaux et al. “Detection of brain functional-connectivity difference in post-stroke patients using group-level covariance modeling, MICCAI 2010.

Attributes

`cov_estimator_`(estimator object) A new covariance estimator with the same parameters as cov_estimator.
`mean_`(numpy.ndarray) The mean connectivity matrix across subjects. For ‘tangent’ kind, it is the geometric mean of covariances (a group covariance matrix that captures information from both correlation and partial correlation matrices). For other values for “kind”, it is the mean of the corresponding matrices
`whitening_`(numpy.ndarray) The inverted square-rooted geometric mean of the covariance matrices.
__init__(cov_estimator=LedoitWolf(store_precision=False), kind='covariance', vectorize=False, discard_diagonal=False)

Initialize self. See help(type(self)) for accurate signature.

fit(X, y=None)

Fit the covariance estimator to the given time series for each subject.

Parameters:

X : list of numpy.ndarray, shape for each (n_samples, n_features)

The input subjects time series. The number of samples may differ from one subject to another.

Returns:

self : ConnectivityMatrix instance

The object itself. Useful for chaining operations.

fit_transform(X, y=None, confounds=None)

Fit the covariance estimator to the given time series for each subject. Then apply transform to covariance matrices for the chosen kind.

Parameters:

X : list of n_subjects numpy.ndarray with shapes (n_samples, n_features)

The input subjects time series. The number of samples may differ from one subject to another.

confounds : np.ndarray with shape (n_samples) or (n_samples, n_confounds), or pandas DataFrame, optional

Confounds to be cleaned on the vectorized matrices. Only takes into effect when vetorize=True. This parameter is passed to signal.clean. Please see the related documentation for details.

Returns:

output : numpy.ndarray, shape (n_subjects, n_features, n_features) or (n_subjects, n_features * (n_features + 1) / 2) if vectorize is set to True.

The transformed individual connectivities, as matrices or vectors. Vectors are cleaned when vectorize=True and confounds are provided.

get_params(deep=True)

Get parameters for this estimator.

Parameters:

deep : bool, default=True

If True, will return the parameters for this estimator and contained subobjects that are estimators.

Returns:

params : mapping of string to any

Parameter names mapped to their values.

inverse_transform(connectivities, diagonal=None)

Returns connectivity matrices from connectivities, vectorized or not.

If kind is ‘tangent’, the covariance matrices are reconstructed.

Parameters:

connectivities : list of n_subjects numpy.ndarray with shapes (n_features, n_features) or (n_features * (n_features + 1) / 2,)

or ((n_features - 1) * n_features / 2,) Connectivities of each subject, vectorized or not.

diagonal : numpy.ndarray, shape (n_subjects, n_features), optional

The diagonals of the connectivity matrices.

Returns:

output : numpy.ndarray, shape (n_subjects, n_features, n_features)

The corresponding connectivity matrices. If kind is ‘correlation’/ ‘partial correlation’, the correlation/partial correlation matrices are returned. If kind is ‘tangent’, the covariance matrices are reconstructed.

set_params(**params)

Set the parameters of this estimator.

The method works on simple estimators as well as on nested objects (such as pipelines). The latter have parameters of the form <component>__<parameter> so that it’s possible to update each component of a nested object.

Parameters:

**params : dict

Estimator parameters.

Returns:

self : object

Estimator instance.

transform(X, confounds=None)

Apply transform to covariances matrices to get the connectivity matrices for the chosen kind.

Parameters:

X : list of n_subjects numpy.ndarray with shapes (n_samples, n_features)

The input subjects time series. The number of samples may differ from one subject to another.

confounds : numpy.ndarray with shape (n_samples) or (n_samples, n_confounds), optional

Confounds to be cleaned on the vectorized matrices. Only takes into effect when vetorize=True. This parameter is passed to signal.clean. Please see the related documentation for details.

Returns:

output : numpy.ndarray, shape (n_subjects, n_features, n_features) or (n_subjects, n_features * (n_features + 1) / 2) if vectorize is set to True.

The transformed individual connectivities, as matrices or vectors. Vectors are cleaned when vectorize=True and confounds are provided.