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##. (If the first
       transformation in the sequence is inverted, then '--inverse' must  be  preceded  by  '--',
       i.e., use '-- --inverse xform.path').

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]

       --pad-floating <double>
            Padding value for the floating image [Default: disabled]

   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, Daniel B. Russakoff, and Yaroslav Halchenko

LICENSE

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

BUGS

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

ACKNOWLEDGMENTS

       CMTK is developed with support from the NIAAA under Grant AA021697, National Consortium on
       Alcohol  and  Neurodevelopment  in Adolescence (N-CANDA): Data Integration Component. From
       April 2009 through September 2011, CMTK development and maintenance was supported  by  the
       NIBIB under Grant EB008381.