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.