table of contents
film(1) | The Computational Morphometry Toolkit | film(1) |
NAME¶
film - Fix interleaved motion using inverse interpolation
SYNOPSIS¶
film InputImage OutputImage
DESCRIPTION¶
This tool splits an interleaved input image into the pass images, co-registers them, and reconstructs a motion-corrected image
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.
- --xml
- Write command line syntax specification in XML markup (for Slicer integration).
- --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 Options¶
- --padding-value <double>
- Set padding value for input image. Pixels with this value will be ignored. [Default: disabled]
Interleaving Options¶
- --interleave-axis
- Define interleave axis: this is the through-slice direction of the acquisition. Supported values: "guess-from-input", "axial", "sagittal", "coronal", "interleave-x", "interleave-y", "interleave-z", where the default is "guess-from-input", or use one of the following:
- --guess-from-input
- Guess from input image [This is the default]
- --axial, -a
- Interleaved axial images
- --sagittal, -s
- Interleaved sagittal images
- --coronal, -c
- Interleaved coronal images
- --interleave-x, -x
- Interleaved along x axis
- --interleave-y, -y
- Interleaved along y axis
- --interleave-z, -z
- Interleaved along z axis
- --passes <integer>, -p <integer>
- Number of interleaved passes [Default: 2]
- --pass-weight <string>, -W <string>
- Set contribution weight for a pass in the form 'pass:weight'
Motion Correction / Registration Options¶
- --reference-image <image-path>, -R <image-path>
- Use a separate high-resolution reference image for registration [Default: NONE]
- --registration-metric
- Registration metric for motion estimation by image-to-image registration. Supported values: "nmi", "mi", "cr", "msd", "cc", where the default is "msd", or use one of the following:
- --nmi
- Use Normalized Mutual Information for pass-to-refereence registration
- --mi
- Use standard Mutual Information for pass-to-refereence registration
- --cr
- Use Correlation Ratio for pass-to-refereence registration
- --msd
- Use Mean Squared Differences for pass-to-refereence registration [This is the default]
- --cc
- Use Cross-Correlation for pass-to-refereence registration
- --import-xforms-path <path>
- Path of file from which to import transformations between passes. [Default: NONE]
- --export-xforms-path <path>
- Path of file to which to export transformations between passes. [Default: NONE]
Initial Volume Injection Options¶
- --injection-kernel-sigma <double>, -S <double>
- Standard deviation of Gaussian kernel for volume injection in multiples of pixel size in each direction. [Default: 0.5]
- --injection-kernel-radius <double>, -r <double>
- Truncation radius factor of injection kernel. The kernel is truncated at sigma*radius, where sigma is the kernel standard deviation. [Default: 2]
Inverse Interpolation Options¶
- --inverse-interpolation-kernel
- Kernel for the inverse interpolation reconstruction Supported values: "cubic", "linear", "hamming-sinc", "cosine-sinc", where the default is "cubic", or use one of the following:
- --cubic, -C
- Tricubic interpolation [This is the default]
- --linear, -L
- Trilinear interpolation (faster but less accurate)
- --hamming-sinc, -H
- Hamming-windowed sinc interpolation
- --cosine-sinc, -O
- Cosine-windowed sinc interpolation (most accurate but slowest)
- --fourth-order-error, -f
- Use fourth-order (rather than second-order) error for optimization.
- --num-iterations <integer>, -n <integer>
- Maximum number of inverse interpolation iterations [Default: 20]
Reconstruction Regularization Options¶
- --l-norm-weight <double>
- Set constraint weight for Tikhonov-type L-Norm regularization (0 disables constraint) [Default: 0]
- --no-truncation, -T
- Turn off regional intensity truncatrion
Output Options¶
- --write-injected-image <image-path>
- Write initial volume injection image to path [Default: NONE]
- --write-images-as-float, -F
- Write output images as floating point [default: same as input]
AUTHORS¶
Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko
LICENSE¶
BUGS¶
Report bugs at http://nitrc.org/projects/cmtk/
ACKNOWLEDGMENTS¶
CMTK 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.
Jul 7 2024 | CMTK 3.3.1p2 |