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fslr (version 1.3)

fslmask: Mask image using FSL

Description

This function calls fslmaths -mas to mask an image from an image mask and either saves the image or returns an object of class nifti

Usage

fslmask(file, mask, outfile = NULL, retimg = FALSE, reorient = FALSE,
  intern = TRUE, opts = "", verbose = TRUE, ...)

Arguments

file
(character) image to be masked
mask
(character) mask given for image
outfile
(character) resultant masked image name
retimg
(logical) return image of class nifti
reorient
(logical) If retimg, should file be reoriented when read in? Passed to readNIfTI.
intern
(logical) to be passed to system
opts
(character) additional options to be passed to fslmask
verbose
(logical) print out command before running
...
additional arguments passed to readNIfTI.

Value

  • Result from system command, depends if intern is TRUE or FALSE. if (have.fsl()){ system.time({ x = array(rnorm(1e6), dim = c(100, 100, 100)) img = nifti(x, dim= c(100, 100, 100), datatype = convert.datatype()$FLOAT32, cal.min = min(x), cal.max = max(x), pixdim = rep(1, 4)) mask = img > .5 masked = fslmask(img, mask = mask, retimg=TRUE) }) }