fslslicetimer {fslr}

FSL Slice Timing Correction

Description

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

Usage

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