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epiunwarp - Unwarp Echo Planar Images


epiunwarp InputImage1 InputImage2 OutputImage1 OutputImage2 OutputDField OutputDFieldRev


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


Global Toolkit Options (these are shared by all CMTK tools)
Write list of basic command line options to standard output.

Write complete list of basic and advanced command line options to standard output.

Write list of command line options to standard output in MediaWiki markup.

Write man page source in 'nroff' markup to standard output.

Write toolkit version to standard output.

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
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

--phase-encode-is, -z
Top/bottom phase encoding (this is rare)

--phase-encode-lr, -x
Lateral, left/right phase encoding (this is extremely rare)

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
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]


Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R.
Maurer, Daniel B. Russakoff, and Yaroslav Halchenko

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