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.

--no-jacobian-correct-global

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] (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

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.