cmtk-pxsearch - Online in the Cloud

PROGRAM:

NAME

pxsearch - Search image neighborhoods for pixels.

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

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