mia-3dmotioncompica-nonrigid(1)

Usage

mia-3dmotioncompica-nonrigid -i <in-file> -o <out-file> [options]

Overview

mia-3dmotioncompica-nonrigid This program implements a 3D version of the motion compensation algorithm described in

Wollny G, Kellman P, Santos A, Ledesma-Carbayo M-J, "Automatic Motion Compensation of Free Breathing acquired Myocardial Perfusion Data by using Independent Component Analysis" Medical Image Analysis, 2012 ⟨https://doi.org/10.1016/j.media.2012.02.004⟩

Options

File-IO

-i --in-file=(required, input); io: input images of consecutively numbered filed (nameXXXX.ext)
For supported file types see PLUGINS:3dimage/io

-o --out-file=(required, output); io: output image name (as C format string including a %04d in order to define the file numbering)
For supported file types see PLUGINS:3dimage/io

--save-refs=: save reference images, the given string is used as file name base, the number pattern follows the input images, and the output format is always 'vista'

--save-regs=: save intermediate registered images, the given string is used as file name base, the number pattern follows the input images, and the output format is always 'vista'

--save-coeffs=: save mixing matrix to a text file

--save-features=: save feature images as PNG

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

Ica

--fastica=internal: FastICA implementationto be used
For supported plugins see PLUGINS:fastica/implementation

-C --components=0: ICA components 0 = automatic estimation

--no-normalize: don't normalized ICs

--no-meanstrip: don't strip the mean from the mixing curves

-k --skip=0: skip images at the beginning of the series e.g. because as they are of other modalities

-m --max-ica-iter=400: maximum number of iterations in ICA

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

-O --optimizer=gsl:opt=gd,step=0.1: Optimizer used for minimization

-a --start-c-rate=32: start coefficinet rate in spines, gets divided by --c-rate-divider with every pass

--c-rate-divider=4: cofficient rate divider for each pass

-d --start-divcurl=20: start divcurl weight, gets divided by --divcurl-divider with every pass

--divcurl-divider=4: divcurl weight scaling with each new pass

-w --imagecost=image:weight=1,cost=ssd,: image cost

-l --mg-levels=3: multi-resolution levels

-P --passes=3: registration passes

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: fastica/implementation

internal: This is the MIA implementation of the FastICA algorithm.

(no parameters)

itpp: This is the IT++ implementation of the FastICA algorithm.

(no parameters)

Examples

Register the perfusion series given in images imagesXXXX.v by using 4-class ICA estimation. Skip two images at the beginning, use at most 4 registration threads, a nlopt based optimizer and otherwiese use the default parameters. Store the result in registeredXXXX.v

mia-3dmotioncompica-nonrigid -i images0000.v -o registered%04d.v -k 2 -C 4 -t 4 -O nlopt:opt=ld-var1,xtola=0.001,ftolr=0.001,maxiter=300

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)

--fastica since Debian 10 (Buster).