fslr: fslepi_reg – R documentation

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fslepi_reg

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

fslr

Wrapper Functions for 'FSL' ('FMRIB' Software Library) from Functional MRI of the Brain ('FMRIB')

v2.24.1

GPL-3

Authors

John Muschelli [aut, cre] (<https://orcid.org/0000-0001-6469-1750>)

Initial release