Resample an Image to Specific Voxel Size

fsl_resample(
  file,
  voxel_size,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  opts = NULL,
  verbose = TRUE
)

Arguments

file: Input file to resample
voxel_size: Voxel size (in mm). This should be a scalar number.
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.
opts: options to pass to flirt
verbose: (logical) print out command before running

Value

If retimg then object of class nifti. Otherwise, the output file.

Examples

if (have_fsl()) {
file = mni_fname(mm = 1, brain = TRUE)
est2 = fsl_resample(file = file, voxel_size = 1, retimg = FALSE)
pixdim(est2)
est = fsl_resample(file = file, voxel_size = 1)
pixdim(est)
}
#> flirt -in "/usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz"  -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -applyisoxfm 1 -out "/var/folders/1s/wrtqcpxn685_zk570bnx9_rr0000gr/T//RtmpKzob0N/file85756130b58a";
#> flirt -in "/usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz"  -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -applyisoxfm 1 -out "/var/folders/1s/wrtqcpxn685_zk570bnx9_rr0000gr/T//RtmpKzob0N/file857544dea8df";
#> [1] -1  1  1  1  1  1  1  1