mia-2dmyoperiodic-nonrigid

mia-2dmyoperiodic-nonrigid
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Sysnopis:

mia-2dmyoperiodic-nonrigid {-i string} {-o string} [ options ...]

Description:

This program runs the non-rigid registration of an perfusion image series preferable acquired letting the patient breath freely. The registration algorithm implementes

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); string: input perfusion data set
-o, --out-file=(required, output); string: output perfusion data set
-r, --registered=reg; stringSTRING: file name base for registered fiels
--save-references: Save synthetic references to files refXXXX.v

Preconditions

-k, --skip=0; ulong: Skip images at the begin of the series
--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: 2dimage/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
--refiner=: optimizer used for additional minimization. For supported plug-ins see Plugin type: minimizer/singlecost
-l, --mr-levels=3; ulong: multi-resolution levels
-f, --transForm=spline:rate=16,penalty=[divcurl:weight=0.01]; factory: transformation type. For supported plug-ins see Plugin type: 2dimage/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: 2dimage/fullcost
-2, --cost-final=image:cost=ssd; factory: Cost function for registration during the final registration. For supported plug-ins see Plugin type: 2dimage/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:

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

--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 perfusion series given in 'segment.set'. Skip two images at the beginning, usa spline transformation of a knot rate 16 pixels, and penalize the transformation by divcurl with weight 5. Store the result in 'registered.set'.

mia-2dmyoperiodic-nonrigid   -i segment.set -o registered.set -k 2 -d 5 -f spline:rate=16,penalty=[divcurl:weight=5]

Author(s):

Gert Wollny

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