Man page - cmtk-epiunwarp(1)

Packages contains this manual

Manual

epiunwarp

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
Global Toolkit Options (these are shared by all CMTK tools)
Input Image Parameters
Optimization Parameters
Output Options
AUTHORS
LICENSE
BUGS
ACKNOWLEDGMENTS

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.