cmtk-reformatx (1)

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)

--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]

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

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

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

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.