FSL ROI

This function calls fslroi

fslroi(
  file,
  xmin = 0,
  xsize = -1,
  ymin = 0,
  ysize = -1,
  zmin = 0,
  zsize = -1,
  tmin = NULL,
  tsize = NULL,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  verbose = TRUE,
  ...
)

fsl_roi(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

fslroi_time(file, tmin = NULL, tsize = NULL, ...)

Arguments

file

(character) image to be manipulated

xmin

Minimum index for x-dimension

xsize

Size of ROI in x-dimension

ymin

Minimum index for y-dimension

ysize

Size of ROI in y-dimension

zmin

Minimum index for z-dimension

zsize

Size of ROI in z-dimension

tmin

Minimum index for t-dimension

tsize

Size of ROI in t-dimension

outfile

(character) resultant image name (optional)

retimg

(logical) return image of class nifti

reorient

(logical) If retimg, should file be reoriented when read in? Passed to readnii.

intern

(logical) to be passed to system

verbose

(logical) print out command before running

...

additional arguments passed to readnii.

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

Note

Indexing (in both time and space) starts with 0 not 1! Inputting -1 for a size will set it to the full image extent for that dimension.