fslmaths erode

# FSL: fsl dilate or fsl erode: 
# Kernel operations (set BEFORE filtering operation if desired): 
# -kernel 3D : 3x3x3 box centered on target voxel (set as default kernel)
# -kernel 2D : 3x3x1 box centered on target voxel 
# Spatial Filtering operations: 
# N.B. all options apart from -s use the default kernel or that 
# previously specified by -kernel 
# -dilM : Mean Dilation of non-zero voxels 
# -dilD : Modal Dilation of non-zero voxels 
# -dilF : Maximum filtering of all voxels 
# -dilall : Apply -dilM repeatedly until the entire FOV is covered 
# -ero : Erode by zeroing non-zero voxels when zero voxels found in kernel 
# -eroF : Minimum filtering of all voxels 

# dilation example 
# -odt sets the output data type. 
# odt options are char short int float double
fslmaths mask -kernel 3D -dilM mask -odt short

# erosion example
fslmaths mask -kernel 2D -ero mask -odt short