mia-3dfluid(1)

Usage

mia-3dfluid -i <in-image> -r <ref-image> -o <out-transformation> [options]

Overview

mia-3dfluid This program is used for non-rigid registration based on fluid dynamics as described in:

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 image
For supported file types see PLUGINS:3dimage/io

-r --ref-image=(input, required); io: reference image
For supported file types see PLUGINS:3dimage/io

-o --out-transformation=(output, required); io: output transformation comprising the registering transformation field
For supported file types see PLUGINS:3dtransform/io

-d --out-image=(output); io: save deformed image
For supported file types see PLUGINS:3dimage/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

--disable-multigrid: disable multi-grid processing

--disable-fullres: disable processing on the full resolution image

--lambda=1: elasticy constant

--mu=1: elasticy constant

-s --start-size=16: initial multigrided size

-m --method=sora: method for solving PDE

sor ‐ successive overrelaxation

sora ‐ Gauss Southwell relexation

--step=0.8: Initial stepsize

-p --interpolator=bspline:d=3: image interpolator kernel
For supported plugins see PLUGINS:1d/splinekernel

--relax=1: overrelaxation factor vor method sor

--maxiter=10: maximum iterations

--epsilon=0.01: truncation condition

--matter=4: intensity above which real matter is assumed (experimental)

PLUGINS: 1d/splinekernel

bspline: B-spline kernel creation , supported parameters are:

d = 3; int in [0, 5]

Spline degree.

omoms: OMoms-spline kernel creation, supported parameters are:

d = 3; int in [3, 3]

Spline degree.

PLUGINS: 3dimage/io

analyze: 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

datapool: Virtual IO to and from the internal data pool

Recognized file extensions: .@

dicom: Dicom image series as 3D

Recognized file extensions: .DCM, .dcm

Supported element types:

signed 16 bit, unsigned 16 bit

hdf5: 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: 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

mhd: 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: 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: VFF Sun raster format

Recognized file extensions: .VFF, .vff

Supported element types:

unsigned 8 bit, signed 16 bit

vista: 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

vti: 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

vtk: 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

PLUGINS: 3dtransform/io

bbs: Binary (non-portable) serialized IO of 3D transformations

Recognized file extensions: .bbs

datapool: Virtual IO to and from the internal data pool

Recognized file extensions: .@

vista: Vista storage of 3D transformations

Recognized file extensions: .v, .v3dt

xml: XML serialized IO of 3D transformations

Recognized file extensions: .x3dt

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-3dfluid -i test.v -r ref.v -o regfield.v -s 16

AUTHOR(s)

Gert Wollny

History

Debian 12 (Bookworm): the text shown here
Debian 11 (Bullseye)
Debian 10 (Buster)
Debian 9 (Stretch)
Debian 8 (Jessie)