mia-2dmyoset-all2one-nonrigid(1) | General Commands Manual | mia-2dmyoset-all2one-nonrigid(1) |
NAME¶
mia-2dmyoset-all2one-nonrigid - Non-linear registration of a series of 2D images.
SYNOPSIS¶
mia-2dmyoset-all2one-nonrigid -i <in-file> -o <out-file> [options] <PLUGINS:2dimage/fullcost>
DESCRIPTION¶
mia-2dmyoset-all2one-nonrigid This program runs non-rigid registration of a series of images given in an image set. All images are registered to one user defined reference image.
OPTIONS¶
File-IO¶
- -i --in-file=(required, input); string
- input perfusion data set
- -o --out-file=(required, output); string
- output perfusion data set
- --out-filebase=reg
- file name basae for registered files, file type is deducted from the image file type in the input data set.
Registration¶
- -k --skip=0
- Skip images at the beginning of the series
- -O --optimizer=gsl:opt=gd,step=0.1
- Optimizer used for minimization
- -l --mg-levels=3
- multi-resolution levels
- -f --transForm=spline
- transformation type
For supported plugins see PLUGINS:2dimage/transform - -r --ref=-1
- reference frame (-1 == use image in the middle)
Help & Info¶
- -V --verbose=warning
- verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:
- --copyright
- print copyright information
- -h --help
- print this help
- -? --usage
- print a short help
- --version
- print the version number and exit
Processing¶
- --threads=-1
- Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).
PLUGINS: 1d/splinebc¶
- mirror
- Spline interpolation boundary conditions that mirror on the boundary
- repeat
- Spline interpolation boundary conditions that repeats the value at the boundary
- zero
- Spline interpolation boundary conditions that assumes zero for values outside
PLUGINS: 1d/splinekernel¶
- bspline
- B-spline kernel creation , supported parameters are:
- omoms
- OMoms-spline kernel creation, supported parameters are:
PLUGINS: 2dimage/cost¶
- lncc
- local normalized cross correlation with masking support., supported parameters are:
- lsd
- Least-Squares Distance measure
- mi
- Spline parzen based mutual information., supported parameters are:
- ncc
- normalized cross correlation.
- ngf
- This function evaluates the image similarity based on normalized gradient fields. Various evaluation kernels are available., supported parameters are:
- ssd
- 2D imaga cost: sum of squared differences, supported parameters are:
- ssd-automask
- 2D image cost: sum of squared differences, with automasking based on given thresholds, supported parameters are:
PLUGINS: 2dimage/fullcost¶
- image
- Generalized image similarity cost function that also handles multi-resolution processing. The actual similarity measure is given es extra parameter., supported parameters are:
- labelimage
- Similarity cost function that maps labels of two images and handles label-preserving multi-resolution processing., supported parameters are:
- maskedimage
- Generalized masked image similarity cost function that also handles multi-resolution processing. The provided masks should be densly filled regions in multi-resolution procesing because otherwise the mask information may get lost when downscaling the image. The reference mask and the transformed mask of the study image are combined by binary AND. The actual similarity measure is given es extra parameter., supported parameters are:
PLUGINS: 2dimage/io¶
- bmp
- BMP 2D-image input/output support. The plug-in supports reading and writing of binary images and 8-bit gray scale images. read-only support is provided for 4-bit gray scale images. The color table is ignored and the pixel values are taken as literal gray scale values.
- datapool
- Virtual IO to and from the internal data pool
- dicom
- 2D image io for DICOM
- exr
- a 2dimage io plugin for OpenEXR images
- jpg
- a 2dimage io plugin for jpeg gray scale images
- png
- a 2dimage io plugin for png images
- raw
- RAW 2D-image output support
- tif
- TIFF 2D-image input/output support
- vista
- a 2dimage io plugin for vista images
PLUGINS: 2dimage/maskedcost¶
- lncc
- local normalized cross correlation with masking support., supported parameters are:
- mi
- Spline parzen based mutual information with masking., supported parameters are:
- ncc
- normalized cross correlation with masking support.
- ssd
- Sum of squared differences with masking.
PLUGINS: 2dimage/transform¶
- affine
- Affine transformation (six degrees of freedom)., supported parameters are:
- rigid
- Rigid transformations (i.e. rotation and translation, three degrees of freedom)., supported parameters are:
- rotation
- Rotation transformations (i.e. rotation about a given center, one degree of freedom)., supported parameters are:
- spline
- Free-form transformation that can be described by a set of B-spline coefficients and an underlying B-spline kernel., supported parameters are:
- translate
- Translation only (two degrees of freedom), supported parameters are:
- vf
- This plug-in implements a transformation that defines a translation for each point of the grid defining the domain of the transformation., supported parameters are:
PLUGINS: 2dtransform/splinepenalty¶
- divcurl
- divcurl penalty on the transformation, supported parameters are:
EXAMPLE¶
Register the perfusion series given in segment.set by optimizing a spline based transformation with a coefficient rate of 16 pixel using Mutual Information and penalize the transformation by using divcurl with aweight of 2.0.
mia-2dmyoset-all2one-nonrigid -i segment.set -o registered.set
-f spline:rate=16,penalty=[divcurl:weight=2.0] image:cost=mi,weight=2.0
AUTHOR(s)¶
Gert Wollny
COPYRIGHT¶
This software is Copyright (c) 1999‐2015 Leipzig, Germany and Madrid, Spain. It comes with ABSOLUTELY NO WARRANTY and you may redistribute it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 (or later). For more information run the program with the option '--copyright'.
v2.4.7 | USER COMMANDS |