SYNOPSIS

pxsearch InputImage

DESCRIPTION

This tool reads an image file, as well as a list of pixel coordinates from standard input. For each pixel, a local neighbourhood in the image is searched for the maximum value. The location of the maximum is then written to standard output.

OPTIONS

Global Toolkit Options (these are shared by all CMTK tools)

--help

Write list of basic command line options to standard output.

--help-all

Write complete list of basic and advanced command line options to standard output.

--wiki

Write list of command line options to standard output in MediaWiki markup.

--man

Write man page source in 'nroff' markup to standard output.

--version

Write toolkit version to standard output.

--echo

Write the current command line to standard output.

--verbose-level <integer>

Set verbosity level.

--verbose, -v

Increment verbosity level by 1 (deprecated; supported for backward compatibility).

--threads <integer>

Set maximum number of parallel threads (for POSIX threads and OpenMP).

Main Options

--input-coordinates

Coordinate specification mode for program input. Supported values: "absolute", "indexed", "relative", "physical", where the default is "absolute", or use one of the following:

--absolute

Use absolute volume coordinates. For each dimension, the valid range is [0,FOV]. [This is the default]

--indexed

Use grid indexes to specify coordinates. For each dimension, the valid value range is [0,Dims-1].

--relative

Use relative volume coordinates. For each dimension, the valid range is [0,1].

--physical

Use physical volume coordinates. Each given location is transformed into image coordinates via the inverse of the images's index-to-physical space matrix.

--output-coordinates

Coordinate specification mode for program output. Supported values: "absolute", "indexed", "relative", "physical", where the default is "absolute", or use one of the following:

--absolute

Use absolute volume coordinates. For each dimension, the valid range is [0,FOV]. [This is the default]

--indexed

Use grid indexes to specify coordinates. For each dimension, the valid value range is [0,Dims-1].

--relative

Use relative volume coordinates. For each dimension, the valid range is [0,1].

--physical

Use physical volume coordinates. Each given location is transformed into image coordinates via the inverse of the images's index-to-physical space matrix.

--radius <string>

Radius of the search region in pixels (specified either as triple "rX,rY,rZ", or a single value, "rXYZ"). The region searched is [2*rX+1,2*rY+1,2*rZ+1] pixels large, centered at the input location (but cropped at the image boundary). [Default: 1]

--no-reorient

Disable image reorientation into RAS alignment.

AUTHORS

Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko

LICENSE

http://www.fsf.org/licensing/licenses/gpl.html

ACKNOWLEDGMENTS

CMTK is developed with support from the NIAAA under Grant AA021697, National Consortium on Alcohol and Neurodevelopment in Adolescence (N-CANDA): Data Integration Component. From April 2009 through September 2011, CMTK development and maintenance was supported by the NIBIB under Grant EB008381.