Description Usage Arguments Value
View source: R/CT_Skull_Strip.R
Skull Stripping (using FSL's BET) a CT file using fslr
functions
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | 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,
...
)
|
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 |
inskull_mesh |
(logical) Create inskull_mesh file from bet?
(Warning - will take longer)
This an exterior surface of the brain. (experimental)
Also, if |
retimg |
(logical) return image of class nifti |
reorient |
(logical) If retimg, should file be reoriented when read in?
Passed to |
intern |
(logical) pass to |
betcmd |
(character) bet command to be used, see |
opts |
(character) additional options to |
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
|
lthresh |
(default: 0) Lower value to threshold CT
|
uthresh |
(default: 100) Upper value to threshold CT
|
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 |
character or logical depending on intern
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