fsl cluster

#!/bin/sh

# The following examples are used for evaluating binary manual lesion masks
# to identify freckles that should be removed.
  
# Define the connectivity number in terms of
# the way the voxels touch each other (faces, edges, corners): 
# 6 is harshest criterion (only touching faces count as connected), 
# 18 is next (touching faces or edges count),
# 26 is the most lenient connectivity criterion 
# (touching faces, edges, or corners count) 

# List cluster sizes at the designated connectivity  
cluster -i img -t 1 --connectivity=${number}
 
# Create a temporary image (img_cluster_size) with a connectivity of ${number}"
cluster -i img -t 1 --connectivity=${number}  --no_table --osize=img_cluster_size

# Threshold the temporary image and name the output=the original input image
# Note the output data type assumes this is a binary mask. 

fslmaths img_cluster_size -thr ${thresh} -bin img -odt char