Eddy Current Correction

This function calls eddy from FSL for DTI Processing

eddy(
  infile,
  mask,
  acq_file,
  index_file,
  bvecs,
  bvals,
  topup = NULL,
  outfile = NULL,
  retimg = TRUE,
  opts = "",
  verbose = TRUE,
  eddy_cmd = c("eddy", "eddy_openmp", "eddy_cuda"),
  ...
)

Arguments

infile	input filename of 4D image.
mask	Mask filename (or class nifti)
acq_file	A text-file describing the acquisition parameters for the different images in infile The format of this file is identical to that used by topup (though the parameter is called --datain there).
index_file	A text-file that determines the relationship between on the one hand the images in infile and on the other hand the acquisition parameters in acq_file.
bvecs	A text file with normalised vectors describing the direction of the diffusion weighting.
bvals	A text file with b-values describing the "amount of" diffusion weighting
topup	This should only be specified if you have previously run `topup` on your data and should be the same name that you gave as an argument to the --out parameter when you ran topup, aka the base name for output files from topup.
outfile	Output file basename
retimg	(logical) return image of class nifti
opts	Additional options to pass to arguments passed to eddy
verbose	print diagnostic messages
eddy_cmd	The version of eddy to run.
...	Not currently used

Value

Result from system command currently