fsl.wrappers.cluster_commands

This module contains the cluster() function, which calls the FSL cluster / ``fsl-cluster``command.

fsl.wrappers.cluster_commands.cluster(infile, thres, load=True, **kwargs)

Wrapper function for the FSL cluster`/``fsl-cluster) command.

If load is True (the default) a tuple is returned, containing:

• A numpy array containing the cluster table

• A list of column titles

• A dictionary containing references to the standard output as an attribute called stdout, and to the output images if any, e.g. --oindex.

If load is False, only the dictionary is returned.

fsl.wrappers.cluster_commands._cluster(infile, thresh, **kwargs)

Actual wrapper function for the FSL cluster/fsl-cluster command.

fsl.wrappers.cluster_commands.smoothest(inimg=None, **kwargs)

Wrapper for the smoothest command.

The residual or zstatistic image may be passed as the first positional argument (inimg) - its type is inferred from the image file name if possible. If this is not possible (e.g. non-standard file names or in-memory images), you must specify residual images via res, or zstatistic images via zstat.

Returns a dictionary containing the parameters estimated by smoothest, e.g.:

{
    'DLH'       : 1.25903,
    'VOLUME'    : 239991,
    'RESELS'    : 3.69574,
    'FWHMvoxel' : [1.57816, 1.64219, 1.42603],
    'FWHMmm'    : [3.15631, 3.28437, 2.85206]
}

fsl.wrappers.cluster_commands._smoothest(inimg=None, **kwargs)

Actual wrapper for the smoothest command.