histnifti

Description:

A command line tool to generate a histogram for a nifti file

Inputs:

A nifti file

Outputs:

A text file containing the histogram information

None

Usage:

Generates a histogram of the values in a NIFTI file.

usage: histnifti [-h] [--histlen LEN] [--minval MINVAL] [--maxval MAXVAL]
                 [--robustrange] [--transform] [--nozero]
                 [--nozerothresh THRESH] [--normhist] [--maskfile MASK]
                 [--nodisplay]
                 inputfile outputroot

Positional Arguments

inputfile

The name of the input NIFTI file.

outputroot

The root of the output file names.

Named Arguments

--histlen

Set histogram length to LEN (default is to set automatically).

--minval

Minimum bin value in histogram.

--maxval

Maximum bin value in histogram.

--robustrange

Set histogram limits to the data’s robust range (2nd to 98th percentile).

Default: False

--transform

Replace data value with it’s percentile score.

Default: False

--nozero

Do not include zero values in the histogram.

Default: False

--nozerothresh

Absolute values less than this are considered zero. Default is 0.01.

Default: 0.01

--normhist

Return a probability density instead of raw counts.

Default: False

--maskfile

Only process voxels within the 3D mask MASK.

--nodisplay

Do not display histogram.

Default: True