mia-3dprealign-nonrigid

Sysnopis:

mia-3dprealign-nonrigid {-i io} {-o io} [ options ...]

Description:

This program runs the non-rigid registration of an image series by first registering an already aligned subset of the images to one reference, and then by registering the remaining images by using synthetic references. The is a 3D version of G. Wollny, M-J Ledesma-Cabryo, P.Kellman, and A.Santos, "Exploiting Quasiperiodicity in Motion Correction of Free-Breathing," IEEE Transactions on Medical Imaging, 29(8), 2010.

Options:

File-IO

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

input images following the naming pattern nameXXXX.ext. For supported file types see Plugin type: 3dimage/io

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

file name base for registered files given as C-format string. For supported file types see Plugin type: 3dimage/io

--save-references

Save synthetic references to files refXXXX.v

Preconditions & Preprocessing

-k, --skip=0; ulong

Skip images at the begin of the series

--preskip=20; ulong

Skip images at the beginning+skip of the series when searching for high contrats image

--postskip=2; ulong

Skip images at the end of the series when searching for high contrats image

--max-candidates=20; ulong

maximum number of candidates for global reference image

-S, --cost-series=image:cost=[ngf:eval=ds]; factory

Const function to use for the analysis of the series. For supported plug-ins see Plugin type: 3dimage/fullcost

--ref-idx=STRING

save reference index number to this file

-R, --global-reference=-1; int

save reference index number to this file

-D, --max-subset-delta=0; ulong

Maximum delta between two elements of the prealigned subset

Registration

-O, --optimizer=gsl:opt=gd,step=0.01; factory

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

-l, --mr-levels=3; ulong

multi-resolution levels

-f, --transForm=spline; factory

transformation type. For supported plug-ins see Plugin type: 3dimage/transform

-1, --cost-subset=image:cost=[ngf:eval=ds]; factory

Cost function for registration during the subset registration. For supported plug-ins see Plugin type: 3dimage/fullcost

-2, --cost-final=image:cost=ssd; factory

Cost function for registration during the final registration. For supported plug-ins see Plugin type: 3dimage/fullcost

Help & Info

-V, --verbose=warning; dict

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=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

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 image series given by images imageXXXX.v by optimizing a spline based transformation with a coefficient rate of 16 pixel, skipping two images at the beginning and using normalized gradient fields as initial cost measure and SSD as final measure. Penalize the transformation by using divcurl with aweight of 2.0. As optimizer an nlopt based newton method is used.

mia-3dprealign-nonrigid mia-3dprealign-nonrigid  -i imageXXXX.v -o registered -t vista -k 2-F spline:rate=16,penalty=[divcurl:weight=2] -1 image:cost=[ngf:eval=ds] -2 image:cost=ssd -O nlopt:opt=ld-var1,xtola=0.001,ftolr=0.001,maxiter=300

Author(s):

Gert Wollny