cmtk-epiunwarp - Online in the Cloud

PROGRAM:

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

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