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¶
- --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).
- --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).
