multiLabelMorphology.RdWraps calls to iMath binary morphology. Additionally, dilation and closing operations preserve pre-existing labels. The choices of operation are:
multiLabelMorphology(
labelsIn,
operation,
radius,
dilationMask = NULL,
labelList = NA
)Input image should contain only 0 for background and positive integers for labels.
One of 'MD', 'ME', 'MC', 'MO', passed to iMath.
radius of the morphological operation.
Optional binary mask to constrain dilation only (eg dilate cortical label into WM).
Optional list of labels, to perform operation upon. Defaults to all unique
intensities in labels.in.
processed labels, of type antsImage.
Dilation: dilates all labels sequentially, but does not overwrite original labels. This reduces dependence on the intensity ordering of adjoining labels. Ordering dependence can still arise if two or more labels dilate into the same space - in this case, the label with the lowest intensity is retained. With a mask, dilated labels are multiplied by the mask and then added to the original label, thus restricting dilation to the mask region.
Erosion: Erodes labels independently, equivalent to calling iMath iteratively.
Closing: Close holes in each label sequentially, but does not overwrite original labels. Opening: Opens each label independently, equivalent to calling iMath iteratively.
img <- antsImageRead(getANTsRData("r16"), 2)
labels <- getMask(img, 1, 150) + getMask(img, 151, 225) * 2
labelsDilated <- multiLabelMorphology(labels, "MD", 2)
# should see original label regions preserved in dilated version
# label N should have mean N and 0 variance
labelStats(labelsDilated, labels)
#> LabelValue Mean Min Max Variance Count Volume Mass x y
#> 3 0 0.01395981 0 2 0.02578888 64041 64041 0 0.0000 0.0000
#> 1 1 2.00000000 2 2 0.00000000 216 216 432 149.5185 156.9815
#> 2 2 2.00000000 2 2 0.00000000 1279 1279 2558 124.5676 130.9805
#> z t
#> 3 NA NA
#> 1 NA NA
#> 2 NA NA