Scroll to navigation

mia-2dmulti-force(1) General Commands Manual mia-2dmulti-force(1)

NAME

mia-2dmulti-force - Registration force between two images

SYNOPSIS

mia-2dmulti-force -o <out-file> [options] <PLUGINS:2dimage/fullcost>

DESCRIPTION

mia-2dmulti-force This program evaluates the 2D image cost force norm image of a given cost function set. The input images must be of the same dimensions and gray scale (whatever bit-depth).

OPTIONS

output norm image
For supported file types see PLUGINS:2dimage/io

Help & Info

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace ‐ Function call trace
debug ‐ Debug output
info ‐ Low level messages
message ‐ Normal messages
warning ‐ Warnings
fail ‐ Report test failures
error ‐ Report errors
fatal ‐ Report only fatal errors
print copyright information

print this help

-? --usage
print a short help

print the version number and exit

Processing

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/splinekernel

B-spline kernel creation , supported parameters are:

d = 3; int in [0, 5]
Spline degree.

OMoms-spline kernel creation, supported parameters are:

d = 3; int in [3, 3]
Spline degree.

PLUGINS: 2dimage/cost

local normalized cross correlation with masking support., supported parameters are:

w = 5; uint in [1, 256]
half width of the window used for evaluating the localized cross correlation.

Least-Squares Distance measure

(no parameters)
Spline parzen based mutual information., supported parameters are:

cut = 0; float in [0, 40]
Percentage of pixels to cut at high and low intensities to remove outliers.

mbins = 64; uint in [1, 256]
Number of histogram bins used for the moving image.

mkernel = [bspline:d=3]; factory
Spline kernel for moving image parzen hinstogram. For supported plug-ins see PLUGINS:1d/splinekernel

rbins = 64; uint in [1, 256]
Number of histogram bins used for the reference image.

rkernel = [bspline:d=0]; factory
Spline kernel for reference image parzen hinstogram. For supported plug-ins see PLUGINS:1d/splinekernel

normalized cross correlation.

(no parameters)
This function evaluates the image similarity based on normalized gradient fields. Various evaluation kernels are available., supported parameters are:

eval = ds; dict
plugin subtype. Supported values are:
sq ‐ square of difference
ds ‐ square of scaled difference
dot ‐ scalar product kernel
cross ‐ cross product kernel

2D imaga cost: sum of squared differences, supported parameters are:

autothresh = 0; float in [0, 1000]
Use automatic masking of the moving image by only takeing intensity values into accound that are larger than the given threshold.

norm = 0; bool
Set whether the metric should be normalized by the number of image pixels.

2D image cost: sum of squared differences, with automasking based on given thresholds, supported parameters are:

rthresh = 0; double
Threshold intensity value for reference image.

sthresh = 0; double
Threshold intensity value for source image.

PLUGINS: 2dimage/fullcost

Generalized image similarity cost function that also handles multi-resolution processing. The actual similarity measure is given es extra parameter., supported parameters are:

cost = ssd; factory
Cost function kernel. For supported plug-ins see PLUGINS:2dimage/cost

debug = 0; bool
Save intermediate resuts for debugging.

ref =(input, io)
Reference image. For supported file types see PLUGINS:2dimage/io

src =(input, io)
Study image. For supported file types see PLUGINS:2dimage/io

weight = 1; float
weight of cost function.

Similarity cost function that maps labels of two images and handles label-preserving multi-resolution processing., supported parameters are:

debug = 0; int in [0, 1]
write the distance transforms to a 3D image.

maxlabel = 256; int in [2, 32000]
maximum number of labels to consider.

ref =(input, io)
Reference image. For supported file types see PLUGINS:2dimage/io

src =(input, io)
Study image. For supported file types see PLUGINS:2dimage/io

weight = 1; float
weight of cost function.

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:

cost = ssd; factory
Cost function kernel. For supported plug-ins see PLUGINS:2dimage/maskedcost

ref =(input, io)
Reference image. For supported file types see PLUGINS:2dimage/io

ref-mask =(input, io)
Reference image mask (binary). For supported file types see PLUGINS:2dimage/io

src =(input, io)
Study image. For supported file types see PLUGINS:2dimage/io

src-mask =(input, io)
Study image mask (binary). For supported file types see PLUGINS:2dimage/io

weight = 1; float
weight of cost function.

PLUGINS: 2dimage/io

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.

Recognized file extensions: .BMP, .bmp

Supported element types:
binary data, unsigned 8 bit

Virtual IO to and from the internal data pool

Recognized file extensions: .@

2D image io for DICOM

Recognized file extensions: .DCM, .dcm

Supported element types:
signed 16 bit, unsigned 16 bit

a 2dimage io plugin for OpenEXR images

Recognized file extensions: .EXR, .exr

Supported element types:
unsigned 32 bit, floating point 32 bit

a 2dimage io plugin for jpeg gray scale images

Recognized file extensions: .JPEG, .JPG, .jpeg, .jpg

Supported element types:
unsigned 8 bit

a 2dimage io plugin for png images

Recognized file extensions: .PNG, .png

Supported element types:
binary data, unsigned 8 bit, unsigned 16 bit

RAW 2D-image output support

Recognized file extensions: .RAW, .raw

Supported element types:
binary data, signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit, unsigned 32 bit, floating point 32 bit, floating point 64 bit

TIFF 2D-image input/output support

Recognized file extensions: .TIF, .TIFF, .tif, .tiff

Supported element types:
binary data, unsigned 8 bit, unsigned 16 bit, unsigned 32 bit

a 2dimage io plugin for vista images

Recognized file extensions: .-, .V, .VISTA, .v, .vista

Supported element types:
binary data, signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit, unsigned 32 bit, floating point 32 bit, floating point 64 bit

PLUGINS: 2dimage/maskedcost

local normalized cross correlation with masking support., supported parameters are:

w = 5; uint in [1, 256]
half width of the window used for evaluating the localized cross correlation.

Spline parzen based mutual information with masking., supported parameters are:

cut = 0; float in [0, 40]
Percentage of pixels to cut at high and low intensities to remove outliers.

mbins = 64; uint in [1, 256]
Number of histogram bins used for the moving image.

mkernel = [bspline:d=3]; factory
Spline kernel for moving image parzen hinstogram. For supported plug-ins see PLUGINS:1d/splinekernel

rbins = 64; uint in [1, 256]
Number of histogram bins used for the reference image.

rkernel = [bspline:d=0]; factory
Spline kernel for reference image parzen hinstogram. For supported plug-ins see PLUGINS:1d/splinekernel

normalized cross correlation with masking support.

(no parameters)
Sum of squared differences with masking.

(no parameters)

EXAMPLE

Evaluate the force normimage weighted sum of costs SSD and NGF of image1.v and image2.v. and store the result to force.v.

mia-2dmulti-force -o force.v
image:cost=ssd,src=image1.v,ref=image2.v,weight=0.1
image:cost=ngf,src=image1.v,ref=image2.v,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