get_quickshear_mask: Face Removal Mask using "Quickshear Defacing for Neuroimages"...

In muschellij2/fslr: Wrapper Functions for 'FSL' ('FMRIB' Software Library) from Functional MRI of the Brain ('FMRIB')

Face Removal Mask using "Quickshear Defacing for Neuroimages" (Schimke et al. 2011)

Description

Face Removal Mask using "Quickshear Defacing for Neuroimages" (Schimke et al. 2011)

Usage

get_quickshear_mask(brain_mask, buffer = 10, verbose = TRUE)

quickshear_deface_image(
  file,
  brain_mask = NULL,
  buffer = 10,
  verbose = TRUE,
  ...
)

Arguments

brain_mask	Brain mask image. If NULL, then fslbet will be run
buffer	buffer to add to intercept for face mask equation
verbose	print diagnostic messages
file	input image - same orientation as brain mask
...	additional arguments passed to fslmask

Value

A binary image of the non-face areas

Note

adapted from https://github.com/nipy/quickshear/blob/master/quickshear.py

Examples

if (have_fsl()) {
   file = "~/Downloads/sample_T1_input.nii.gz"
   if (file.exists(file)) {
       res = quickshear_deface_image(file)
       brain_mask = fslbet(file) > 0
       mask = get_quickshear_mask(brain_mask)
       image = fslmask(file, mask)
   }
}

muschellij2/fslr documentation built on Aug. 31, 2022, 8:47 p.m.