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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

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