cmtk-fibxform(1) [debian man page]

fibxform(1)					       The Computational Morphometry Toolkit					       fibxform(1)

NAME

       fibxform - Apply coordinate transformations to point coordinates in .fib file.

SYNOPSIS

       fibxform XformList

DESCRIPTION

       A  file	with fiber tracking results from the UNC Fiber Tracking tool is read from Standard Input and one or more (concatenated) coordinate
       transformations are applied to all fiber point coordinates. The result is written to Standard Output, again in UNC fiber file format.

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
       --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: 0.001]

       --source-image <image-path>
	    Set  source  image of the transformation (i.e., an image defining the space in which fiber tracking was performed) to correct for dif-
	    ferences in orientation and coordinate space.  [Default: NONE]

       --target-image <image-path>
	    Set target image of the transformation (i.e., the image that the fiber track points are mapped into) to  correct  for  differences	in
	    orientation and coordinate space.  [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 						       fibxform(1)

fit_spline_xform(1)				       The Computational Morphometry Toolkit				       fit_spline_xform(1)

NAME

       fit_spline_xform - Fit Single B-Spline Transformation to Concatenated Transformation List

SYNOPSIS

       fit_spline_xform InputImage XformList

DESCRIPTION

       Fit a parametric nonrigid transformation (B-spline free-form deformation) 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).

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

       --fit-affine-first
	    Fit affine transformation first, then initialize spline with it.

       --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  controlpoints)  of  the output B-spline transformation. To be provided as
	    'dimX,dimY,dimZ'.  [Default: NONE]

   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]

   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_spline_xform(1)