mid_sagittal_align: Mid-Sagittal Plane Alignment

In muschellij2/fslr: Wrapper Functions for 'FSL' ('FMRIB' Software Library) from Functional MRI of the Brain ('FMRIB')

Mid-Sagittal Plane Alignment

Description

This function takes in an image, flips the image over the left/right plane, registers that flipped image to the original image, then applies the half transformation

Usage

mid_sagittal_align(
  file,
  opts = "",
  translation = TRUE,
  force_rpi = TRUE,
  verbose = TRUE
)

apply_mid_sagittal_align(
  file,
  file_mat,
  apply_opts = "",
  force_rpi = TRUE,
  verbose = TRUE
)

Arguments

file	(character) input filename or class nifti
opts	(character) options passed to flirt
translation	(logical) should the translation parameters be preserved (TRUE) or set to zero (FALSE)
force_rpi	Should rpi_orient_file be run?
verbose	(logical) print diagnostic messages
file_mat	file name of mat file for half transform from [mid_sagittal_align]
apply_opts	options to pass to [fslr::flirt_apply]

Value

Filename of output or nifti depending on retimg

Examples

if (have.fsl()){
  mnifile = file.path(fsldir(), "data", "standard",
                      "MNI152_T1_2mm.nii.gz")
  aligned = mid_sagittal_align(mnifile)
  thresh = readnii(mnifile) > 0
  file_mat = attr(aligned, "half_transform")
  force_rpi = attr(aligned, "force_rpi")
  flipped_thresh = apply_mid_sagittal_align(
    file = thresh, 
    file_mat = file_mat,
    apply_opts = "-interp nearestneighbour",
    force_rpi = force_rpi
  )
}

muschellij2/fslr documentation built on Feb. 6, 2025, 10 a.m.