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