SYNOPSISepiunwarp InputImage1 InputImage2 OutputImage1 OutputImage2 OutputDField OutputDFieldRev
DESCRIPTIONCorrect 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 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)
- 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.
- 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]
- --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]
AUTHORSTorsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko
BUGSReport bugs at http://nitrc.org/projects/cmtk/
ACKNOWLEDGMENTSCMTK 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.