fslr: flirt – R documentation

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flirt

Description

This function calls flirt to register infile to reffile and either saves the image or returns an object of class nifti, along with the transformation matrix omat

Usage

flirt(infile, reffile, omat = NULL, dof = 6, outfile = NULL,
  retimg = TRUE, reorient = FALSE, intern = FALSE, opts = "",
  verbose = TRUE, ...)

Arguments

`infile`	(character) input filename
`reffile`	(character) reference image to be registered to
`omat`	(character) Output matrix name
`dof`	(numeric) degrees of freedom (default 6 - rigid body)
`outfile`	(character) output filename
`retimg`	(logical) return image of class nifti
`reorient`	(logical) If retimg, should file be reoriented when read in? Passed to `readnii`.
`intern`	(logical) pass to `system`
`opts`	(character) additional options to FLIRT
`verbose`	(logical) print out command before running
`...`	additional arguments passed to `readnii`.

Value

character or logical depending on intern

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