fslr: fnirt_with_affine – R documentation

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fnirt_with_affine

Description

This function calls fnirt to register infile to reffile and either saves the image or returns an object of class nifti, but does the affine registration first

Usage

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

Arguments

`infile`	(character) input filename
`reffile`	(character) reference image to be registered to
`flirt.omat`	(character) Filename of output affine matrix
`flirt.outfile`	(character) Filename of output affine-registered image
`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`
`flirt.opts`	(character) additional options to FLIRT
`opts`	(character) additional options to FNIRT
`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