---
name: "cmtk-reformatx"
section: "1"
platform: "linux"
package: "cmtk"
version: "3.3.1p2+dfsg-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/cmtk-reformatx"
---

# cmtk-reformatx(1)

Volume reformatter

## 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.