createAntsArgs: interface to generate arguments for antsRegistration command
In zarquon42b/RANTs: Playing with ANTs(R)

interface to generate arguments for antsRegistration command

createAntsArgs(reference, target, setting = "custom", percent = 0.1,
  affine = c("trans", "rigid", "similarity", "affine"),
  affinereach = 32, affineconverge = "[10000x10000x10000,1e-8,20]",
  elastic = "SyN[0.2,3,0]", elasticpercent = 0.1,
  elasticconverge = "[100x10x1,0,5]", elasticmetrics = c("mattes",
  "cc"), metricweights = NULL, metricreach = c(32, 4), dims = 3,
  elasticS = "3x1x0vox", elasticF = "3x2x1", initTransform = NULL,
  itkthreads = parallel::detectCores(), masks = NULL, folder = NULL,
  transimg = FALSE, verbose = FALSE)

`reference`	path to moving image
`target`	path to fixed image
`setting`	name of the setting to be attached to output
`percent`	subsampling for affine transforms
`affine`	character vector of non-elastic transform to use
`affinereach`	character vector assigning the bins for Mattes metric used for affine transforms.
`elastic`	character vector of elastic procedures (including parameters). E.g "SyN[0.2,3,0]"
`elasticmetrics`	character vector containing the metrics to be used in elastic matching
`metricweights`	character vector of same length as `elasticmetrics`, assigning weights to each metric. If NULL, all selected metrics will be weighted equally.
`metricreach`	character vector of same length as `elasticmetrics`, assigning the radius/bins for each metric to consider.
`dims`	dimensionality of data
`elasticS`	smoothing sigmas (see command args of antsRegistration)
`elasticF`	shrink factors (see command args of antsRegistration)
`initTransform`	run initial coarse alignment or provide a transform file. These features include using the geometric center of the images (=0), the image intensities (=1), or the origin of the images (=2) or a list containing lists with two entries containing the path to the transform and a logical indicating if the transform is to be inverted. E.g `initTransform=list(list("mytransfrom.mat",TRUE))`
`itkthreads`	integer: specify number of threads to be used
`folder`	character defining the path where to store the transforms
`transimg`	logical: if TRUE the diff and inv will be created.
`verbose`	logcal: if TRUE output are written to console
`affineconvergence`	character: convergence values for affine transforms MxNxO [MxNxO,<convergenceThreshold=1e-6>,<convergenceWindowSize=10>]
`elasticconvergence`	character: convergence valzes MxNxO [MxNxO,<convergenceThreshold=1e-6>,<convergenceWindowSize=10>]