pixelcomp

Description:

A program to compare voxel values in two 3D NIFTI files. You give pixelcomp two files, each with their own mask. Any voxel that has a nonzero mask in both files gets added to a list of xy pairs, with the value from the first file being x, and the value from the second file being y. Pixelcomp then: 1) Makes and displays a 2D histogram of all the xy values. 2) Does a linear fit to x and y, and outputs the coefficients (slope and offset) to a XXX_linfit.txt file. 3) Writes all the xy pairs to a tab separated text file, and 4) Makes a Bland-Altman plot of x vs y

Inputs:

Two 3D NIFTI image files, the accompanying mask files, and the root name for the output files.

Outputs:

None

Usage:

Compare two nifti files, voxel by voxel, in a contour plot

usage: pixelcomp [-h] [--scatter] [--fitonly] [--nodisplay] [--fitorder ORDER]
                 [--usex] [--histbins NUM]
                 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

--scatter

Do a scatter plot intstead of a contour plot.

Default: False

--fitonly

Perform fit only - do not generate graph.

Default: False

--nodisplay

Save graphs to file only - do not display.

Default: True

--fitorder

Order of line fit - default is 1 (linear).

Default: 1

--usex

Use x instead of (y + x)/2 in Bland-Altman plot.

Default: False

--histbins

Number of bins per dimension for the contour plot -Default is 51.

Default: 51