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mia-3dforce(1) General Commands Manual mia-3dforce(1)

NAME

mia-3dforce - Evaluate the registration force between two 3D images.

SYNOPSIS

mia-3dforce -i <src-file> -r <ref-file> -o <out-file> [options]

DESCRIPTION

mia-3dforce This program is used to create an image comprising the pixel-wise norm of the ggradient of a given cost function.

OPTIONS

input image
For supported file types see PLUGINS:3dimage/io
output force norm image
For supported file types see PLUGINS:3dimage/io
reference image
For supported file types see PLUGINS:3dimage/io
cost function to use
For supported plugins see PLUGINS:3dimage/cost

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: 3dimage/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.

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. Given normalized gradient fields $ _S$ of the src image and $ _R$ of the ref image various evaluators are implemented., supported parameters are:

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

3D image 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.

3D 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: 3dimage/io

Analyze 7.5 image

Recognized file extensions: .HDR, .hdr

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

Virtual IO to and from the internal data pool

Recognized file extensions: .@

Dicom image series as 3D

Recognized file extensions: .DCM, .dcm

Supported element types:
signed 16 bit, unsigned 16 bit

HDF5 3D image IO

Recognized file extensions: .H5, .h5

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

INRIA image

Recognized file extensions: .INR, .inr

Supported element types:
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

MetaIO 3D image IO using the VTK implementation (experimental).

Recognized file extensions: .MHA, .MHD, .mha, .mhd

Supported element types:
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

NIFTI-1 3D image IO. The orientation is transformed in the same way like it is done with 'dicomtonifti --no-reorder' from the vtk-dicom package.

Recognized file extensions: .NII, .nii

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

VFF Sun raster format

Recognized file extensions: .VFF, .vff

Supported element types:
unsigned 8 bit, signed 16 bit

Vista 3D

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

3D image VTK-XML in- and output (experimental).

Recognized file extensions: .VTI, .vti

Supported element types:
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

3D VTK image legacy in- and output (experimental).

Recognized file extensions: .VTK, .VTKIMAGE, .vtk, .vtkimage

Supported element types:
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

EXAMPLE

Evaluate the weigtes sum of SSD between src.v and ref.v and store the result in forcenorm.v.

mia-3dforce -i src.v -r ref.v -c ssd -o forcenorm.v

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