BRAINSia/BRAINSStandAlone — pull request #110 by aghayoor (2012-09-06 16:29:32+00:00)
Title: Add syn registration option to brains fit

Syn option from ANTS is hard coded into BRAINSFit.
To do the SyN registration by the BRAINSFit, we just need "fixedVolume", "movingVolume" and "initialTransform" as the input arguments, and the BRAINSFit does the syn registration with hard coded parameters.
A command line example of using syn registration by BRAINSFit is as follows:

./BRAINSFit \
--initialTransform ANTS_build_directory/ANTS-build/TestData/Initializer_0.05_antsRegistrationTest_AffineScaleMasks.mat \
--useSyN \
--fixedVolume BRAINSStandAlone_build_directory/BRAINSTools-build/TestData/test.nii.gz \
--movingVolume BRAINSStandAlone_build_directory/BRAINSTools-build/TestData/scale.test.nii.gz \
--outputTransform BRAINSFitSyN_outputMask.nii.gz \
--outputVolume BRAINSFitSyN_outputImage.nii.gz