Hi Cathy,
 
I feel that your binary images might be too big. You may want to down-sample your binary objects and see (1) if that solves the problem and (2) if the down-sampled objects still look good enough.
 
You can use "Exercise 2.2: SPHARM-PDM Topology Fix" to achieve this goal:
http://imaging.indyrad.iupui.edu/project...
 
Basically, if you look at the figure "Screen Shot for SPHARM-PDM Topology Fix", you will find an edit box "space" and its default value is "0.75,0.75,0.75". This option defines the resample resolution. You can change it to "2 2 2", "4 4 4" or other numbers (>1) to down-sample the original images.
 
Hope this helps.
 
Best,
 
Li