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:

--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:

--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).