fslepi_reg: Register EPI images to Structural image

In muschellij2/fslr: Wrapper Functions for 'FSL' ('FMRIB' Software Library) from Functional MRI of the Brain ('FMRIB')

Register EPI images to Structural image

Description

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

Usage

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

muschellij2/fslr documentation built on May 10, 2024, 2:12 a.m.