cmtk-xform2itk(1) [debian man page]

xform2itk(1)					       The Computational Morphometry Toolkit					      xform2itk(1)

NAME

       xform2itk - Convert affine transformations to ITK format.

SYNOPSIS

       xform2itk InputPath OutputPath

DESCRIPTION

       This  tool  converts  coordinate  transformations from CMTK format to ITK format and, in the process, also correct for differences in image
       coordinate conventions

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).

   Input parameters
       --fixed-space <string>
	    Change fixed image coordinate space (e.g., 'RAS', 'LPS', ...). This defaults to ITK standard space.  [Default: LPS ]

       --moving-space <string>
	    Change moving image coordinate space (e.g., 'RAS', 'LPS', ...). This defaults to ITK standard space.  [Default: LPS ]

       --invert-input
	    Invert input transformation before conversion

   Output parameters
       --fixed-image <string>
	    Override transformation's fixed/reference image (if any) with this one.  [Default: NONE]

       --moving-image <string>
	    Override transformation's moving/floating image (if any) with this one.  [Default: NONE]

AUTHORS

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

LICENSE

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

BUGS

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

ACKNOWLEDGMENTS

       From April 2009 through September 2011, CMTK Development and Maintenance was supported by the National Institute of Biomedical Imaging  and
       Bioengineering under Grant No.R01 EB008381 (PI: Torsten Rohlfing).

CMTK 2.2.2							    Jul 20 2012 						      xform2itk(1)

detect_adni_phantom(1)				       The Computational Morphometry Toolkit				    detect_adni_phantom(1)

NAME

       detect_adni_phantom - Detect ADNI phantom landmarks in phantom image

SYNOPSIS

       detect_adni_phantom InputImage OutputXML

DESCRIPTION

       This  tool  detects  the  locations  of all spherical landmarks in a 3D image of the Magphan EMR051 structural imaging phantom (a.k.a. ADNI
       Phantom).

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
       --write-labels <image-path>
	    Output label image path. This image contains the mask of detected spheres, each labeled uniquely in their order in CMTK's ADNI phantom
	    fiducial table.  [Default: NONE]

       --write-rigid <transformation-path>
	    Output  path  for  the fitted rigid transformation from phantom space into RAS image standard space. This transformation defines where
	    each sphere should be in the image.  [Default: NONE]

       --write-affine <transformation-path>
	    Output path for the fitted affine transformation from phantom space into RAS image standard space.	This  is  the  closest	linear-fit
	    transformation, and as such it includes scale and shear components not present in the fitted rigid transformations. Since these compo-
	    nents are due to scanner miscalibration and distortion, this transformation DOES NOT specify  the  correct	spehre	locations  in  the
	    image, but rather, allows for quantification of scale miscalibration.  [Default: NONE]

AUTHORS

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

LICENSE

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

BUGS

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

ACKNOWLEDGMENTS

       From  April 2009 through September 2011, CMTK Development and Maintenance was supported by the National Institute of Biomedical Imaging and
       Bioengineering under Grant No.R01 EB008381 (PI: Torsten Rohlfing).

CMTK 2.2.2							    Jul 20 2012 					    detect_adni_phantom(1)