fslr (version 1.9.2.1)

mcflirt: FSL Motion Correction

Description

This function calls mcflirt

Usage

mcflirt(file, outfile = NULL, retimg = TRUE, reorient = FALSE, intern = FALSE, opts = "", verbose = TRUE, ...)

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

opts

(character) operations to be passed to mcflirt. Cannot use -o or -verbose, as output file should be specified in outfile.

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.