epiunwarp(1) The Computational Morphometry Toolkit epiunwarp(1)
NAME
epiunwarp - Unwarp Echo Planar Images
SYNOPSIS
epiunwarp InputImage1 InputImage2 OutputImage1 OutputImage2 OutputDField
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)
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, and Daniel B. Russakoff
LICENSE
http://www.fsf.org/licensing/licenses/gpl.html
BUGS
Report bugs at http://nitrc.org/projects/cmtk/
ACKNOWLEDGMENTS
From April 2009 through September 2011, CMTK Development and Maintenance was supported by the National Institute of Biomedical Imaging and
Bioengineering under Grant No.R01 EB008381 (PI: Torsten Rohlfing).
CMTK 2.2.2 Jul 20 2012 epiunwarp(1)