fslroi: FSL ROI

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

FSL ROI

Description

This function calls fslroi

Usage

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.

muschellij2/fslr documentation built on May 10, 2024, 2:12 a.m.