applytopup {fslr}

applytopup - calling FSL applytopup

Description

A tool for applying and correcting estimated susceptibility induced distortions

Usage

applytopup(
  infile,
  datain,
  index,
  topup_files,
  out = NULL,
  method = c("lsr", "jac"),
  interp = c("spline", "trilinear"),
  verbose = TRUE
)

apply_topup(...)

fsl_applytopup(...)

Arguments

infile

list of names of input image (to be corrected)

datain

name of text file with PE directions/times

index

list of indices into –datain of the input image (to be corrected)

topup_files

name of field/movements (from topup)

out

basename for output (warped) image

method

Use jacobian modulation (jac) or least-squares resampling (lsr), default=lsr.

interp

Image interpolation model, trilinear or spline. Default spline

verbose

Print diagnostic information while running

...

arguments passed to topup if using fsl_topup