debian man page for cmtk-reformatx

reformatx(1)					       The Computational Morphometry Toolkit					      reformatx(1)

NAME
       reformatx - Volume reformatter

SYNOPSIS
       reformatx [options] --floating floatingImg target x0 [x1 ...]
	 OR reformatx [options] target [x0 x1 ...] {-j,--jacobian} xx0 [xx1 ...]
	 OR WHERE x0 ... xN and xx0 ... xxN is [{-i,--inverse}] transformation##

DESCRIPTION
       Extended volume reformatter tool to compute reformatted images and Jacobian maps from arbitrary sequences of concatenated 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).

       --outputtype
	    Scalar  data type for the output image.  Supported values: "char", "byte", "short", "ushort", "int", "uint", "float", "double", or use
	    one of the following:

	    --char
		 8 bits, signed

	    --byte
		 8 bits, unsigned

	    --short
		 16 bits, signed

	    --ushort
		 16 bits, unsigned

	    --int
		 32 bits signed

	    --uint
		 32 bits unsigned

	    --float
		 32 bits floating point

	    --double
		 64 bits floating point

       --pad-out <double>, -P <double>
	    Padding value for output image [Default: 0]

   Options for Plain Reformatting
       --interpolation
	    Image interpolation method.  Supported values: "linear", "nn", "cubic", "pv", "sinc-cosine",  "sinc-hamming",  where  the  default	is
	    "linear", or use one of the following:

	    --linear
		 Trilinear interpolation [This is the default]

	    --nn Nearest neighbor interpolation

	    --cubic
		 Tricubic interpolation

	    --pv Partial volume interpolation

	    --sinc-cosine
		 Sinc interpolation with cosine window

	    --sinc-hamming
		 Sinc interpolation with Hamming window

       --sinc-window-radius <integer>
	    Window radius for Sinc interpolation [Default: 3]

       --preserve-mass
	    Mass-preserving reformatting: multiply every reformatted value with the Jacobian determinant of the applied transformation.

   Options for Jacobian Map Reformatting
       --jacobian-correct-global
	    Correct Jacobian maps for global scale.  [This is the default]

       --no-jacobian-correct-global
	    Do not correct Jacobian maps for global scale.

   Input Options
       --target-grid <string>
	    Define target grid for reformating as Nx,Ny,Nz:dX,dY,dZ[:Ox,Oy,Oz] (dims:pixel:offset)

       --mask, -m
	    Use target pixel data as binary mask.

       --crop <string>
	    Crop target image: x0,y0,z0,x1,y1,z2

       --target-offset <string>, -O <string>
	    Override target image offset and set to x,y,z mm

       --target-offset-pixels <string>
	    Override target image offset and set to dx,dy,dz pixels

       --floating <string>, -F <string>
	    Format and path of floating image.	[Default: NONE]

   Output Options
       --outfile <string>, -o <string>
	    Format and path of output image.  [Default: reformat.nii ]

   Image/Transformation Database
       --db <string>
	    Path to image/transformation database that should be updated with the newly created image.	[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 						      reformatx(1)