Description Usage Arguments Value Note
View source: R/CT_Skull_Strip_robust.R
Skull Stripping (using FSL's BET) a CT file
using fslr
functions and robustified by registration
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 | 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
)
|
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 |
retimg |
(logical) return image of class nifti |
reorient |
(logical) If retimg, should file be
reoriented when read in?
Passed to |
int |
Fractional Intensity passed to
|
lthresh |
(default: 0) Lower value to threshold CT
|
uthresh |
(default: 100) Upper value to threshold CT
|
nvoxels |
Number of voxels to dilate/erode.
See |
remove.neck |
Run |
remover |
if |
smooth.factor |
Smoothing factor for |
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
|
template.mask |
Mask of template to use as rough
brain mask, passed
to |
... |
additional arguments passed to
|
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
|
Skull-stripped nifti
object
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.
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