---
name: "cmtk-pxsearch"
section: "1"
platform: "linux"
package: "cmtk"
version: "3.3.1p2+dfsg-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/cmtk-pxsearch"
---

# cmtk-pxsearch(1)

Search image neighborhoods for pixels.

## 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

## LICENSE

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

## BUGS

Report bugs at http://nitrc.org/projects/cmtk/

## 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.