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cmtk-unwarp_image_phantom(1) [debian 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)

Check Out this Related Man Page

fit_affine_xform(1)				       The Computational Morphometry Toolkit				       fit_affine_xform(1)

NAME

       fit_affine_xform - Fit Single Affine Transformation to Concatenated List

SYNOPSIS

       fit_affine_xform InputImage XformList

DESCRIPTION

       Fit a linear affine transformation to a list of concatenated, optionally inverted, transformations.

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 Options
       --inversion-tolerance <double>
	    Numerical  tolerance  of B-spline inversion in mm. Smaller values will lead to more accurate inversion, but may increase failure rate.
	    [Default: 1e-08]

   Fitting Options
       --rigid
	    Fit rigid transformation (rotation and translation only) using SVD.

       --affine
	    Fit full affine transformation (rotation, translation, scales, shears) using pseudoinverse.  [This is the default]

   Output Options
       --output <transformation-path>, -o <transformation-path>
	    Path for the output transformation.  [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 					       fit_affine_xform(1)
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