Mask image using FSL

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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

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fslmask(file, mask, outfile = NULL, retimg = TRUE, reorient = FALSE,
  intern = FALSE, 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 readnii.

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 readnii.

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) )

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