mne.stats.spatio_temporal_cluster_test

mne.stats.spatio_temporal_cluster_test(X, threshold=1.67, n_permutations=1024, tail=0, stat_fun=<function f_oneway>, connectivity=None, verbose=None, n_jobs=1, seed=None, max_step=1, spatial_exclude=None, step_down_p=0, t_power=1, out_type='indices', check_disjoint=False, buffer_size=1000)

Non-parametric cluster-level test for spatio-temporal data

This function provides a convenient wrapper for data organized in the form (observations x time x space) to use permutation_cluster_test.

Parameters:

X: list of arrays

Array of shape (observations, time, vertices) in each group.

threshold: float

The threshold for the statistic.

n_permutations: int

See permutation_cluster_test.

tail : -1 or 0 or 1 (default = 0)

See permutation_cluster_test.

stat_fun : function

function called to calculate statistics, must accept 1d-arrays as arguments (default: scipy.stats.f_oneway)

connectivity : sparse matrix or None

Defines connectivity between features. The matrix is assumed to be symmetric and only the upper triangular half is used. Default is None, i.e, a regular lattice connectivity.

verbose : bool, str, int, or None

If not None, override default verbose level (see mne.verbose).

n_jobs : int

Number of permutations to run in parallel (requires joblib package).

seed : int or None

Seed the random number generator for results reproducibility.

max_step : int

When connectivity is a n_vertices x n_vertices matrix, specify the maximum number of steps between vertices along the second dimension (typically time) to be considered connected. This is not used for full or None connectivity matrices.

spatial_exclude : list of int or None

List of spatial indices to exclude from clustering.

step_down_p : float

To perform a step-down-in-jumps test, pass a p-value for clusters to exclude from each successive iteration. Default is zero, perform no step-down test (since no clusters will be smaller than this value). Setting this to a reasonable value, e.g. 0.05, can increase sensitivity but costs computation time.

t_power : float

Power to raise the statistical values (usually f-values) by before summing (sign will be retained). Note that t_power == 0 will give a count of nodes in each cluster, t_power == 1 will weight each node by its statistical score.

out_type : str

For arrays with connectivity, this sets the output format for clusters. If ‘mask’, it will pass back a list of boolean mask arrays. If ‘indices’, it will pass back a list of lists, where each list is the set of vertices in a given cluster. Note that the latter may use far less memory for large datasets.

check_disjoint : bool

If True, the connectivity matrix (or list) will be examined to determine of it can be separated into disjoint sets. In some cases (usually with connectivity as a list and many “time” points), this can lead to faster clustering, but results should be identical.

buffer_size: int or None

The statistics will be computed for blocks of variables of size “buffer_size” at a time. This is option significantly reduces the memory requirements when n_jobs > 1 and memory sharing between processes is enabled (see set_cache_dir()), as X will be shared between processes and each process only needs to allocate space for a small block of variables.

Returns:

T_obs : array of shape [n_tests]

T-statistic observed for all variables

clusters : list

List type defined by out_type above.

cluster_pv: array

P-value for each cluster

H0 : array of shape [n_permutations]

Max cluster level stats observed under permutation.

Notes

Reference: Cluster permutation algorithm as described in Maris/Oostenveld (2007), “Nonparametric statistical testing of EEG- and MEG-data” Journal of Neuroscience Methods, Vol. 164, No. 1., pp. 177-190. doi:10.1016/j.jneumeth.2007.03.024