fslr: fnirt_with_affine_apply – R documentation

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fslr

fnirt_with_affine_apply

Applies FLIRT then FNIRT transformations

Description

Applies an affine transformation with FLIRT then the warp image with FNIRT

Usage

fnirt_with_affine_apply(infile, reffile, flirt.omat = NULL,
  flirt.outfile = NULL, fnirt.warpfile = 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
`fnirt.warpfile`	(character) Filename of warp image from `fnirt`
`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