fslr (version 1.9.2.1)

fslthresh: Threshold an image

Description

This function calls fslmaths -thr -uthr to threshold an image and either saves the image or returns an object of class nifti

Usage

fslthresh(file, outfile = NULL, thresh = 0, uthresh = NULL, retimg = TRUE, reorient = FALSE, intern = FALSE, opts = "", verbose = TRUE, ...)

Arguments

file

(character) filename of image to be thresholded

outfile

(character) name of resultant thresholded file

thresh

(numeric) threshold (anything below set to 0)

uthresh

(numeric) upper threshold (anything above set to 0)

retimg

(logical) return image of class nifti

reorient

(logical) If retimg, should file be reoriented when read in? Passed to readnii.

intern

(logical) pass to system

opts

(character) additional options to be passed to fslmaths

verbose

(logical) print out command before running

...

additional arguments passed to readnii.

Value

character or logical depending on intern

Examples

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))
thresh = fslthresh(img, thresh=0, uthresh = 2, retimg=TRUE)
})
}