AFNI 3dAllineate function — afni

Wrapper for AFNI 3dAllineate function

afni_3dAllineate(file, fixed, cost = c("hel", "ls", "mi", "crM", "nmi",
  "crA", "crU"), interpolator = c("linear", "cubic", "NN", "quintic"),
  final_interpolator = c("cubic", "linear", "NN", "wsinc5", "quintic"),
  typeOfTransform = c("affine_general", "shift_only", "shift_rotate",
  "shift_rotate_scale"), outfile = NULL, retimg = TRUE, opts = "",
  ...)

allineate(...)

Arguments

file	nifti object or NIfTI filename to register to `fixed` image
fixed	nifti object or NIfTI filename of fixed image, target of registration
cost	cost function that defines the matching between the file and the fixed image ls= Least Squares [Pearson Correlation] mi = Mutual Information [H(b)+H(s)-H(b,s)] crM = Correlation Ratio (Symmetrized*) nmi = Normalized MI [H(b,s)/(H(b)+H(s))] hel = Hellinger metric crA = Correlation Ratio (Symmetrized+) crU = Correlation Ratio (Unsym)
interpolator	interpolation method to use during matching process NN - nearest neighbor.
final_interpolator	interpolation used to create the output dataset. `wsinc5` - weighted sinc interpolation method
typeOfTransform	transformation to use for registration shift_only - 3 parameters shift_rotate - 6 parameters shift_rotate_scale - 9 parameters affine_general - 12 parameters
outfile	Output filename (should not have an extension)
retimg	Should an image be returned (`TRUE`) or a filename?
opts	Additional options passed to `3dAllineate`
...	additional arguments to `afni_3dAFNItoNIFTI`

Value

Output filename of the brik