Use imerode.
From Matlab documentation:
IM2 = imerode(IM,SE) erodes the grayscale, binary, or packed binary image IM, returning the eroded image IM2. The argument SE is a structuring element object or array of structuring element objects returned by the strel function.
Example:
Erode a binary image with a disk structuring element.
originalBW = imread('circles.png');
se = strel('disk',11);
erodedBW = imerode(originalBW,se);
imshow(originalBW), figure, imshow(erodedBW)
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