mia-2dfluid1
Fluid dynamic 2d registration
Usage
mia-2dfluid -i
<in-image>
-r
<ref-image>
[options]
Overview
mia-2dfluid This program is used for non-rigid registration based on fluid dynamics. For reference see
Wollny, G. and Kruggel, F., 'Computational cost of non-rigid registration algorithms based on fluid dynamics', IEEE Transactions on Medical Imaging, 11(8), pp. 946-952, 2002. ⟨https://doi.org/10.1109/TMI.2002.803113⟩
It uses SSD as the sole registration criterion.
Options
File-IO
- -i --in-image=(input, required); io
-
input (test) image to be registered
For supported file types see PLUGINS:2dimage/io
- -r --ref-image=(input, required); io
-
reference image
For supported file types see PLUGINS:2dimage/io
- -o --out-transformation=(output); io
-
output transformation comprising the registration
For supported file types see PLUGINS:2dvf/io
- -d --out-image=(output); io
-
output image deformed according to the transformation
For supported file types see PLUGINS:2dimage/io
Help & Info
- -V --verbose=warning
-
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
-
--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).
Registration parameters
- -m --mgstart=16
-
multigrid start size
- -e --epsilon=0.001
-
optimization breaking condition
-
--mu=1 -
elasticity parameter
-
--lambda=1 -
elasticity parameter
-
--elastic -
use elastic registration
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.
Recognized file extensions: .BMP, .bmp
Supported element types:
binary data, unsigned 8 bit
datapool-
Virtual IO to and from the internal data pool
Recognized file extensions: .@
dicom-
2D image io for DICOM
Recognized file extensions: .DCM, .dcm
Supported element types:
signed 16 bit, unsigned 16 bit
exr-
a 2dimage io plugin for OpenEXR images
Recognized file extensions: .EXR, .exr
Supported element types:
unsigned 32 bit, floating point 32 bit
jpg-
a 2dimage io plugin for jpeg gray scale images
Recognized file extensions: .JPEG, .JPG, .jpeg, .jpg
Supported element types:
unsigned 8 bit
png-
a 2dimage io plugin for png images
Recognized file extensions: .PNG, .png
Supported element types:
binary data, unsigned 8 bit, unsigned 16 bit
raw-
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
tif-
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
vista-
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: 2dvf/io
datapool-
Virtual IO to and from the internal data pool
Recognized file extensions: .@
exr-
a 2dvf io plugin for OpenEXR vfs
Recognized file extensions: .EXR, .exr
Supported element types:
unsigned 32 bit, floating point 32 bit
vista-
a 2d vector field io plugin for vista
Recognized file extensions: .V, .VF, .v, .vf
Supported element types:
floating point 32 bit
Examples
Register image test.v to image ref.v and write the deformation vector field regfield.v. Start registration at the smallest size above 16 pixel.
mia-2dfluid -i test.v -r ref.v -o regfield.v -s 16
AUTHOR(s)
Gert Wollny
History
- Debian 12 (Bookworm) to Debian 11 (Bullseye): the text shown here
- Debian 10 (Buster)
- Debian 9 (Stretch)
- Debian 8 (Jessie)