Register EPI images to Structural image

This function calls epi_reg, designed to register EPI images (typically functional or diffusion) to structural (e.g. T1-weighted) image.

fslepi_reg(
  epi,
  t1,
  t1_brain,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  fmap = NULL,
  fmap_mag = NULL,
  fmap_mag_brain = NULL,
  echo_spacing = NA,
  phase_enc_dir = c("x", "y", "z", "-x", "-y", "-z"),
  weight = NULL,
  verbose = TRUE,
  opts = "",
  ...
)

fsl_epi_reg(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

epi_reg(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

Arguments

epi: EPI image, character or nifti object
t1: whole head T1 image , character or nifti object
t1_brain: brain extracted T1 image
outfile: output registered image filename
retimg: (logical) return image of class nifti
reorient: (logical) If retimg, should file be reoriented when read in? Passed to readnii.
intern: (logical) to be passed to system
fmap: fieldmap image (in rad/s)
fmap_mag: fieldmap magnitude image - whole head extracted
fmap_mag_brain: fieldmap magnitude image - brain extracted
echo_spacing: Effective EPI echo spacing (sometimes called dwell time) - in seconds
phase_enc_dir: phase encoding direction, dir = x/y/z/-x/-y/-z
weight: weighting image (in T1 space)
verbose: (logical) print out command before running
opts: (character) operations to be passed to fslmaths
...: additional arguments passed to readnii.

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping