Hello,

I have been using shapeworks to landmark six different mouse molars.  Shapeworks was run twice on each molar, with identical parameters and volumes.  The results are surprisingly different.  Regressing the distance to the mean shape of each the landmarks configuration between runs, 5-10 samples are drastically different.  See attached plot.  I was wondering if I am running the samples with enough iterations?  I am going to experiment with increasing the number of iteration to see if the results stabilize, but would greatly appreciate any suggestions.  The top of the groom.xml and run.xml files are below.

groom.xml

<?xml version="1.0" encoding="UTF-8"?>
<blur_sigma>0.5</blur_sigma>
<antialias_iterations>50</antialias_iterations>
<background>0</background>
<foreground>2</foreground>
<transform_file>/cm/shared/data/n2_molars/shapeworks/label1//shapeworks.transform</transform_file>
<inputs>/cm/shared/data/n2_molars/shapeworks/label1/def_152-11_to_atlas.nii.gz_inv.nii.gz

run.xml
<?xml version="1.0" encoding="UTF-8"?>
<iterations_per_split>100</iterations_per_split>
<starting_regularization>1000</starting_regularization>
<ending_regularization>0.1</ending_regularization>
<number_of_particles>1024</number_of_particles>
<optimization_iterations>1000</optimization_iterations>
<output_points_prefix>/cm/shared/data/n2_molars/shapeworks/label1//output_points</output_points_prefix>
<output_transform_file>/cm/shared/data/n2_molars/shapeworks/label1//output_transform_file</output_transform_file>
<inputs>/