CT Skull Stripping within R

Skull Stripping (using FSL's BET) a CT file using fslr functions

CT_Skull_Strip(
  img,
  outfile = NULL,
  keepmask = TRUE,
  maskfile = NULL,
  inskull_mesh = FALSE,
  retimg = TRUE,
  reorient = FALSE,
  intern = TRUE,
  betcmd = "bet2",
  opts = "-f 0.01 -v",
  presmooth = TRUE,
  remask = TRUE,
  refill = FALSE,
  refill.thresh = 0.75,
  sigma = 1,
  lthresh = 0,
  uthresh = 100,
  smooth_before_threshold = FALSE,
  verbose = TRUE,
  ...
)

Arguments

img	(character) File to be skull stripped or object of class nifti
outfile	(character) output filename
keepmask	(logical) Should we keep the mask?
maskfile	(character) Filename for mask (if keepmask = TRUE). If NULL, then will do paste0(outfile, "_Mask").
inskull_mesh	(logical) Create inskull_mesh file from bet? (Warning - will take longer) This an exterior surface of the brain. (experimental) Also, if outfile is NULL, then this will be created in a temporary directory and not be retrieved.
retimg	(logical) return image of class nifti
reorient	(logical) If retimg, should file be reoriented when read in? Passed to readNIfTI.
intern	(logical) pass to system
betcmd	(character) bet command to be used, see fslbet
opts	(character) additional options to fslbet
presmooth	(logical) indicator if pre-smoothing should be done before BET
remask	(logical) Mask the smoothed image with HU mask from initial step?
refill	(logical) indicator to post-smooth mask and then fill
refill.thresh	(numeric) Value to threshold post-smoothed mask
sigma	(integer) size of Gaussian kernel passed to fslsmooth if presmooth is TRUE
lthresh	(default: 0) Lower value to threshold CT fslthresh
uthresh	(default: 100) Upper value to threshold CT fslthresh
smooth_before_threshold	Should the image be smoothed before thresholding? This can be useful for bone-window scans.
verbose	(logical) Should diagnostic output be printed?
...	additional arguments passed to fslbet.

Value

character or logical depending on intern