spatialmi

Description:

Inputs:

Outputs:

Usage:

Calculate the localized spatial mutual information between two images

usage: spatialmi [-h] [--noprebin] [--nonorm] [--radius RADIUS]
                 [--sigma SIGMA] [--kernelwidth WIDTH] [--spherical]
                 [--index1 INDEX1] [--index2 INDEX2] [--debug]
                 inputfilename1 maskfilename1 inputfilename2 maskfilename2
                 outputroot

Positional Arguments

inputfilename1

The name of the first input image nifti file.

maskfilename1

The name of the first input mask nifti file.

inputfilename2

The name of the second input image nifti file.

maskfilename2

The name of the second input mask nifti file.

outputroot

The root name of the output files.

Named Arguments

--noprebin

Dynamically calculate histogram bins for each voxel (slower).

Default: True

--nonorm

Do not normalize neighborhood by the variance.

Default: True

--radius

Radius of the comparison, in voxels. If not spherical, comparison neighborhood is cubic with (2 * RADIUS + 1)^3 voxels. Must be 1.0 or greater. Default is 2.0

Default: 2.0

--sigma

Width, in voxels, of a gaussian smoothing filter to apply to each input dataset. Default is no filteriing.

--kernelwidth

Kernel width, in voxels, of gaussian neighborhood limit. Default is no kernel.

--spherical

Use a spherical (rather than cubical) neighborhood (much slower).

Default: False

--index1

If input file 1 is 4 dimensional, select timepoint INDEX1 for spatial mutual information calculation.If not specified, the first image will be used.

Default: 0

--index2

If input file 2 is 4 dimensional, select timepoint INDEX2 for spatial mutual information calculation.If not specified, the first image will be used.

Default: 0

--debug

Print additional internal information.

Default: False