* The programs( which take name=value args ) can now take arguments in both the following forms:
** program-name( <comma-separated-list-of-arguments> )
eg: antsMotionCorr( "-d" , 3 , "-o" , "[" , "foo" , moco_img , avg_img , "]" , "-m" , "MI[" , avg_img , img , 1 , 32 , 50 , "]" , "-t" , "Rigid[0.01]" , "-i" , 25 , "-u" , 1 , "-e" , 1 , "-s" , 0 , "-f" , 1 , "-n" , 25 )
** program-name( <named-list-of-arguments> )
eg: antsMotionCorr( list( d = 3 , o = list( moco_params , moco_img , avg_img ) , m = list( name = "MI" , avg_img , img , 1 , 32 , 50 ) , t = "Rigid[0.01]" , i = 25 , u = 1 , e = 1 , s = 0 , f = 1 , n = 25 ) )
The second form is better and makes more sense.
* The programs can now accept and return multiple images.
Example is in the following script for 'Atropos'.
* The programs can now return data directly to R instead of writing csv files.
Example is in the following script for 'antsMotionCorr'.

The following script gives an example using the above changes:
library(ANTsR)
img = antsImageRead( "KKI2009-01-fMRI.nii" , "float" , 4 )
avg_img = new( "antsImage" , "float" , 3 )
antsMotionCorr( list( d = 3 , a = img , o = avg_img ) )
moco_img = new( "antsImage" , "float" , 4 )
moco_params = new( "antsMatrix" , "double" )
antsMotionCorr( list( d = 3 , o = list( moco_params , moco_img , avg_img ) , m = list( name = "MI" , avg_img , img , 1 , 32 , 50 ) , t = "Rigid[0.01]" , i = 25 , u = 1 , e = 1 , s = 0 , f = 1 , n = 25 ) )
bm_img = new( "antsImage" , "float" , 3 )
ThresholdImage( 3 , avg_img , bm_img , "Otsu" , 3 )
ThresholdImage( 3 , bm_img , bm_img , 2 , 3 )
ImageMath( 3 , bm_img , "ME" , bm_img , 1 )
ImageMath( 3 , bm_img , "GetLargestComponent" , bm_img )
ImageMath( 3 , bm_img , "MD" , bm_img , 1 )
ImageMath( 3 , bm_img , "ME" , bm_img , 1 )
compcorr_corr_img = new( "antsImage" , "float" , 4 )
compcorr_var_img = new( "antsImage" , "float" , 3 )
ImageMath( 4 , antsImagePair( compcorr_corr_img , compcorr_var_img ) , "CompCorrAuto" , moco_img , bm_img , 6 )
N3BiasFieldCorrection( 3 , avg_img , avg_img , 2 , bm_img )
N3BiasFieldCorrection( 3 , avg_img , avg_img , 1 , bm_img )
N3BiasFieldCorrection( 3 , avg_img , avg_img , 1 , bm_img )
N3BiasFieldCorrection( 3 , avg_img , avg_img , 1 , bm_img )
bm_img_uint = antsImageClone( bm_img , "unsigned int" )
seg_img_uint = new( "antsImage" , "unsigned int" , 3 )
Atropos( list( d = 3 , a = avg_img , a = compcorr_var_img , m = "[0.3,1x1x1]" , o = seg_img_uint , c = "[5,0]" , i = "kmeans[3]" , x = bm_img_uint ) )
prob_img_list = new( "antsImageList" , "float" , 3 )
Atropos( list( d = 3 , a = avg_img , a = compcorr_var_img , m = "[0.3,1x1x1]" , o = list( seg_img_uint , prob_img_list ) , c = "[5,0]" , i = "kmeans[3]" , x = bm_img_uint ) )
Atropos( list( d = 3 , a = avg_img , a = compcorr_var_img , m = "[0.3,1x1x1]" , o = list( seg_img_uint , prob_img_list ) , c = "[5,0]" , i = list( name = "priorprobabilityimages" , 3 , prob_img_list , 0 ) , x = bm_img_uint ) )
seg_img_float = antsImageClone( seg_img_uint , "float" )
cortmask_img = new( "antsImage" , "float" , 3 )
ThresholdImage( 3 , seg_img_float , cortmask_img , 2 , 2 )
cortmask_img_double = antsImageClone( cortmask_img , "double" )
moco_img_double = antsImageClone( moco_img , "double" )
mat = new( "antsMatrix" , "double" )
sccan( list( "timeseriesimage-to-matrix" = list( moco_img_double , cortmask_img_double , 0.0 , 0.0  ) , o = mat ) )

The output 'moco_params' of program 'antsMotionCorr' is available in R as an object that can be converted to a list or a data-frame:
moco_params_df = as.data.frame( moco_params )
moco_params_lst = as.list( moco_params )
From a list or data.frame, R provides a lot of functions to convert to other type of R objects. We can manipulate those objects and convert them back to 'antsMatrix' as follows.
mod_moco_params_df = as.data.frame( <modified moco-params in some R object> )
moco_params = as.antsMatrix( mod_moco_params_df )
mod_moco_params_lst = as.list( <modified moco-params in some R object> )
moco_params = as.antsMatrix( mod_moco_params_lst )
Same is true with the output 'mat' of 'sccan' above. The data is available as a list or data-frame and can be converted and manipulated and converted back to 'antsMatrix', which can then be fed to other programs.
updated svn tag for ANTs in CMakeLists.txt