Fill image holes with dilation then erosion

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Description

This function calls fslmaths to dilate an image, then calls it again to erode it.

Usage

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fslfill2(file, outfile = NULL, kopts = "", remove.ends = TRUE,
  refill = TRUE, retimg = TRUE, reorient = FALSE, intern = FALSE,
  verbose = TRUE, ...)

Arguments

file

(character) filename of image to be filled

outfile

(character) name of resultant filled file

kopts

(character) Options passed for kernel before erosion/dilation

remove.ends

(logical) Remove top and bottom dilation.

refill

(logical) Run fslfill after dilation/erosion.

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

verbose

(logical) print out command before running

...

additional arguments passed to readnii.

Value

character or logical depending on intern

Note

This function binarizes the image before running.

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