FSL Slice Timing Correction

Source: R/fsl_slicetimer.R

This function calls slicetimer and performs slice timing correction for fMRI data

fslslicetimer(
  file,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  tr = 3,
  direction = "z",
  indexing = c("up", "down"),
  acq_order = c("contiguous", "interleaved"),
  verbose = TRUE,
  ...
)

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

Arguments

file

(character) image to be manipulated
outfile

(character) resultant image name (optional)
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
tr

(numeric) Repeat time in seconds
direction

(character) Direction of acquisition
indexing

(character) Whether indexing was bottom up (default) or down using --down option
acq_order

(character) Order of acquisition, either contiguous or interleaved
verbose

(logical) print out command before running
...

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