fslr: mcflirt – R documentation

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mcflirt

FSL Motion Correction

This function calls mcflirt

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

`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`.

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

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