Provided by: cmtk_3.2.2-1.4_amd64 bug


       reformatx - Volume reformatter


       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').


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


   Global Toolkit Options (these are shared by all CMTK tools)
            Write list of basic command line options to standard output.

            Write complete list of basic and advanced command line options to standard output.

            Write list of command line options to standard output in MediaWiki markup.

            Write man page source in 'nroff' markup to standard output.

            Write toolkit version to standard output.

            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).

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

                 8 bits, signed

                 8 bits, unsigned

                 16 bits, signed

                 16 bits, unsigned

                 32 bits signed

                 32 bits unsigned

                 32 bits floating point

                 64 bits floating point

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

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

                 Trilinear interpolation [This is the default]

            --nn Nearest neighbor interpolation

                 Tricubic interpolation

            --pv Partial volume interpolation

                 Sinc interpolation with cosine window

                 Sinc interpolation with Hamming window

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

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

   Options for Jacobian Map Reformatting
            Correct Jacobian maps for global scale.

            Do not correct Jacobian maps for global scale.  [This is the default]

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

       --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]


       Torsten  Rohlfing,  with  contributions  from  Michael  P. Hasak, Greg Jefferis, Calvin R.
       Maurer, Daniel B. Russakoff, and Yaroslav Halchenko



       Report bugs at


       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.