mia-2dgroundtruthreg

Sysnopis:

mia-2dgroundtruthreg {-i string} {-o string} {-A double} {-B double} {-R double} [ options ...]

Description:

This program implements the non-linear registration based on Pseudo Ground Thruth for motion compensation of series of myocardial perfusion images as decribed in Chao Li and Ying Sun, 'Nonrigid Registration of Myocardial Perfusion MRI Using Pseudo Ground Truth' , In Proc. Medical Image Computing and Computer-Assisted Intervention MICCAI 2009, 165-172, 2009. Note that for this nonlinear motion correction a preceding linear registration step is usually required.

Options:

File-IO

-i, --in-file=(input,required)

input perfusion data set

-o, --out-file=(output,required)

output perfusion data set

-r, --registered=reg

file name base for registered files

Preconditions

-s, --skip=2

skip images at beginning of series

-P, --passes=4

number of registration passes

Pseudo-Ground-Thruth

-A, --alpha=(required)

spacial neighborhood penalty weight

-B, --beta=(required)

temporal second derivative penalty weight

-R, --rho_thresh=(required)

crorrelation threshhold for neighborhood analysis

Registration

-O, --optimizer=gsl:opt=gd,step=0.1

Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost

-p, --interpolator=bspline:d=3

image interpolator kernel. For supported plug-ins see Plugin type: 1d/splinekernel

-l, --mr-levels=3

multi-resolution levels

-d, --divcurl=20

divcurl regularization weight

--divcurl-divider=4

divcurl weight scaling with each new pass

-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

-w, --imageweight=1

image cost weight

Help & Info

-V, --verbose=warning

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

info:Low level messages
trace:Function call trace
fail:Report test failures
warning:Warnings
error:Report errors
debug:Debug output
message:Normal messages
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).

Example:

Register the perfusion series given by images imageXXXX.exr by using Pseudo Ground Truth estimation. Skip two images at the beginning and otherwiese use the default parameters. Store the result images to 'regXXXX.exr'.

mia-2dgroundtruthreg -i imageXXXX.exr -o regXXXX.exr -k 2

Author(s):

Gert Wollny