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

# cmtk-epiunwarp(1)

Unwarp Echo Planar Images

## NAME

epiunwarp - Unwarp Echo Planar Images

## SYNOPSIS

**epiunwarp** InputImage1 InputImage2 OutputImage1 OutputImage2 OutputDField OutputDFieldRev

## DESCRIPTION

Correct B0 field inhomogeneity-induced distortion in Echo Planar Images (e.g., diffusion-weighted images) using two images acquired with opposing phase encoding directions.

## 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).

### Input Image Parameters

- **--phase-encode**

  Define the phase-encoded image coordinate direction. Supported values: "phase-encode-ap", "phase-encode-is", "phase-encode-lr", where the default is "phase-encode-ap", or use one of the following:

  - **--phase-encode-ap**, **-y**

    Anterior/posterior phase encoding (this is the most common case) **\[This is the default\]**

  - **--phase-encode-is**, **-z**

    Top/bottom phase encoding (this is rare)

  - **--phase-encode-lr**, **-x**

    Lateral, left/right phase encoding (this is extremely rare)

- **--no-flip**

  Use this switch is the reverse phase-encoded image does not need to be flipped prior to unwarping. If normal and reverse phase-encoded image display in the same gross orientation in 'triplanar', then flipping is not necessary and must be turned off using this switch.

### Optimization Parameters

- **--no-init-shift-com**

  Disable initialization of unwarping by shifting each row to align the centers of mass of forward and reverse acquisition. Instead, use all-zero initial deformation field.

- **--smooth-sigma-max** *\<double\>*

  Maximum image smoothing kernel width for coarsest level of multi-scale computation. **\[Default: 8\]**

- **--smooth-sigma-min** *\<double\>*

  Minimum image smoothing kernel width for finest level of multi-scale computation (0 = no smoothing; original image scale). **\[Default: 0\]**

- **--smooth-sigma-diff** *\<double\>*

  Difference between image smoothing kernel widths between two successive levels of the multi-scale computation. **\[Default: 0.25\]**

- **--smoothness-constraint-weight** *\<double\>*

  Weight factor for the second-order smoothness constraint term in the unwarping cost function. **\[Default: 0\]**

- **--folding-constraint-weight** *\<double\>*

  Weight factor for the folding-prevention constraint term in the unwarping cost function. **\[Default: 0\]**

- **--iterations** *\<integer\>*, **-i** *\<integer\>*

  Number of L-BFGS optimization iterations (per multi-scale level). **\[Default: 10\]**

### Output Options

- **--write-jacobian-fwd** *\<string\>*

  Write Jacobian intensity correction map for forward image. **\[Default: NONE\]**

- **--write-jacobian-rev** *\<string\>*

  Write Jacobian intensity correction map for reverse-encoded 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.