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reformatx - Volume reformatter

reformatx(1) The Computational Morphometry Toolkit reformatx(1)

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.
--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

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.
Sep 11 2017 CMTK 3.3.1