afni_3dAllineate: AFNI 3dAllineate function

In neuroconductor-devel/afnir: Wrapper Functions for 'AFNI' (Analysis of Functional 'NeuroImages')

AFNI 3dAllineate function

Description

Wrapper for AFNI 3dAllineate function

Usage

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

neuroconductor-devel/afnir documentation built on June 15, 2025, 3:29 a.m.