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cmtk-detect_adni_phantom(1) [debian man page]

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)

Check Out this Related Man Page

unwarp_image_phantom(1) 			       The Computational Morphometry Toolkit				   unwarp_image_phantom(1)

NAME

       unwarp_image_phantom - Unwarp T1-weighted MR image using a phantom description

SYNOPSIS

       unwarp_image_phantom InputPhantom InputImage OutputXform

DESCRIPTION

       This  tool computes a  B-spline free-form deformation to unwarp an image. The transformation is based on expected and detected landmarks in
       an image of a structural phantom acquired on the same scanner. Use the 'detect_adni_phantom' tool to detect landmarks of the  ADNI  Phantom
       in an image and generate a phantom description file suitable for use with this tool.

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).

   Fitting Options
       --levels <integer>
	    Number of levels in the multi-level B-spline approximation procedure.  [Default: 1]

       --no-fit-affine
	    Disable  fitting  of affine transformation to initialize spline. Instead, fit spline directly. This usually gives worse results and is
	    discouraged.

   Output Options
       --final-cp-spacing <double>
	    Final control point grid spacing of the output B-spline transformation.  [Default: 0]

       --final-cp-dims <string>
	    Final control point grid dimensions (i.e., number of control points)  of  the  output  B-spline  transformation.  To  be  provided	as
	    'dimX,dimY,dimZ'.  [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 					   unwarp_image_phantom(1)
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