fslmaths erode code example
Example: 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