Robust CT Skull Stripping

Skull Stripping (using FSL's BET) a CT file using fslr functions and robustified by registration

CT_Skull_Strip_robust(
  img,
  outfile = NULL,
  keepmask = TRUE,
  maskfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  int = "0.01",
  lthresh = 0,
  uthresh = 100,
  nvoxels = 5,
  remove.neck = TRUE,
  remover = c("remove_neck", "double_remove_neck"),
  smooth.factor = 2,
  recog = TRUE,
  verbose = TRUE,
  opts = NULL,
  mask_to_background = FALSE,
  template.file = system.file("scct_unsmooth_SS_0.01.nii.gz", package = "ichseg"),
  template.mask = system.file("scct_unsmooth_SS_0.01_Mask.nii.gz", package = "ichseg"),
  ...
)

CT_Skull_Strip_register(
  img,
  outfile = NULL,
  keepmask = TRUE,
  maskfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  lthresh = 0,
  uthresh = 100,
  remove.neck = TRUE,
  remover = c("remove_neck", "double_remove_neck"),
  verbose = TRUE,
  mask_to_background = FALSE,
  ...
)

CT_Skull_Strip_smooth(
  img,
  ...,
  smooth_before_threshold = TRUE,
  smooth.factor = 1,
  remove.neck = TRUE,
  remover = c("remove_neck", "double_remove_neck"),
  recog = FALSE,
  nvoxels = 0,
  add_1024 = FALSE
)

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").
retimg	(logical) return image of class nifti
reorient	(logical) If retimg, should file be reoriented when read in? Passed to readNIfTI.
int	Fractional Intensity passed to CT_Skull_Strip and subsequently fslbet.
lthresh	(default: 0) Lower value to threshold CT fslthresh
uthresh	(default: 100) Upper value to threshold CT fslthresh
nvoxels	Number of voxels to dilate/erode. See dil_ero. If nvoxels = 0, then no smoothing is done.
remove.neck	Run remove_neck to register the template to a thresholded image to remove neck slices.
remover	if remove.neck = TRUE, then which function would you like to use to remove the neck
smooth.factor	Smoothing factor for fslbet. See -w option in fslbet.help().
recog	Re-estimate the center of gravity (COG) and skull strip.
verbose	(logical) Should diagnostic output be printed?
opts	Not used
mask_to_background	When masking, should the values outside the mask be set to 0 (default) or -1024 (when TRUE)
template.file	Template to warp to original image space, passed to remove_neck
template.mask	Mask of template to use as rough brain mask, passed to remove_neck
...	additional arguments passed to CT_Skull_Strip or remove_neck.
smooth_before_threshold	Should the image be smoothed before thresholding? This can be useful for bone-window scans.
add_1024	Adding 1024 to the image *before* running the skull stripping. The values are subtracted after. This has interplay with mask_to_background

Value

Skull-stripped nifti object

Note

This function first thresholds an image, runs a rigid registration (default in remove_neck) to drop any slices below the transformed skull stripped template to remove neck slices. The neck-removed image is then skull stripped using defaults in CT_Skull_Strip. A new center of gravity is estiamted using cog, then the image is skull stripped again using the new cog and the smoothness factor (passed to -w argument in BET). After the skull stripped mask is created, the image is dilated and eroded using dil_ero to fill holes using a box kernel with the number of voxels nvoxels in all 3 directions.

CT_Skull_Strip_register removes the neck, registers the image to the template, using a rigid-body transformation, runs the skull stripper to get a mask, then transforms the mask back to native space.