Description Usage Arguments Value Examples
Creates a rough mask of the face from a head scan
1 2 3 4 5 6 7 8 9 10 | ct_face_mask(file, skull_strip = TRUE, mask = NULL, robust = TRUE,
template.file = system.file(ifelse(skull_strip,
"scct_unsmooth_SS_0.01.nii.gz", "scct_unsmooth.nii.gz"), package =
"ichseg"), template.face_mask = NULL,
template.face_mask_inds = list(50:130, 170:217, 1:15),
extend_mask = TRUE, typeofTransform = "Affine", swapdim = TRUE,
verbose = TRUE, ...)
mri_face_mask(..., skull_strip = TRUE, mask = NULL, robust = FALSE,
template.file = mni_fname(brain = skull_strip))
|
file |
File for face masking - either filename or class nifti |
skull_strip |
Should the data require skull stripping if no mask is provided? |
mask |
file or |
robust |
If |
template.file |
Template to warp to original image space |
template.face_mask |
Mask of template to use as rough face mask. If
|
template.face_mask_inds |
List of length 3 for indices of
|
extend_mask |
after transformation, should the mask be extended to the front of the image to ensure all face has been removed? |
typeofTransform |
Transformation for template to image, passed to
|
swapdim |
Should the dimensions be swapped before registration, and then reset after |
verbose |
Print out diagnostic messages |
... |
arguments passed to |
Object of class nifti
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 | ## Not run:
file = "~/Desktop/Desktop/scratch/100-318_20070723_0957_CT_3_CT_Head-.nii.gz"
mask = NULL
robust = FALSE
face = ct_face_mask(
file = file,
robust = FALSE
)
img = readnii(file)
rimg = randomize_mask(img, mask = face)
## End(Not run)
## Not run:
library(fslr)
library(extrantsr)
mri = "~/Desktop/Desktop/scratch/SUBJ0001-01-MPRAGE.nii.gz"
template.file = mni_fname(brain = TRUE)
tmask = mni_fname(brain = TRUE, mask = TRUE)
template.face_mask_inds = list(50:130, 170:217, 1:15)
brain = fslbet_robust(mri,
remove.neck = TRUE,
remover = "double_remove_neck",
template.file = template.file,
template.mask = tmask)
mask = brain > 0
img = brain
template.face_mask = NULL
verbose = TRUE
face = mri_face_mask(
file = img,
mask = mask,
template.file = template.file
)
## End(Not run)
|
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