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[shapeworks-users] Requesting assistance with ShapeWorks Optimization Step


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  • From: Kayley Dear <kayleyd5@gmail.com>
  • To: Shapeworks-users@sci.utah.edu
  • Subject: [shapeworks-users] Requesting assistance with ShapeWorks Optimization Step
  • Date: Mon, 2 Dec 2019 16:48:21 -0500

I am trying to incorporate statistical shape modeling into my Masters Thesis, which is looking at glenohumeral impingement. I have STLs of 17 humeral heads and would like to see if shape correlates with the impingement data we have obtained. 

I've converted the files to .nrrd format with 3D slicer, and can get them through grooming only with center unchecked. The software crashes on the optimization step without moving past 1% though. I was able to run your example of femoral heads, and am not sure where the files differ greatly enough to prevent analysis. I've ensured they all have the same position, and reduced the number of faces greatly but am still having trouble. 

I've attached a couple examples of my data and the project file.

Thanks for any help or suggestions you can provide!
--
Kayley Dear
——————————————————
MSE Candidate, Bioengineering
School of Engineering and Applied Science
University of Pennsylvania | Class of 2019
kayleyd5@gmail.com | kdear@seas.upenn.edu | Cell 856-558-8060
<?xml version="1.0" encoding="UTF-8"?>
<project version="1">
    <cache_enabled>true</cache_enabled>
    <cache_epsilon>0.00100000005</cache_epsilon>
    <cache_memory>25</cache_memory>
    <center_option>true</center_option>
    <color_scheme>0</color_scheme>
    <display_state>Groomed</display_state>
    <glyph_quality>4</glyph_quality>
    <glyph_size>0.80000000000000004</glyph_size>
    <groom_antialias>true</groom_antialias>
    <groom_antialias_amount>10</groom_antialias_amount>
    <groom_blur>true</groom_blur>
    <groom_blur_sigma>2</groom_blur_sigma>
    <groom_center>false</groom_center>
    <groom_crop>false</groom_crop>
    <groom_fastmarching>true</groom_fastmarching>
    <groom_fastmarching_isovalue>0.5</groom_fastmarching_isovalue>
    <groom_fastmarching_sigma>2</groom_fastmarching_sigma>
    <groom_fill_holes>true</groom_fill_holes>
    <groom_isolate>true</groom_isolate>
    <groom_pad>true</groom_pad>
    <groom_pad_value>10</groom_pad_value>
    <neighborhood>9</neighborhood>
    <num_threads>8</num_threads>
    <optimize_clusters>5</optimize_clusters>
    <optimize_decay_span>1000</optimize_decay_span>
    <optimize_decimation>0.29999999999999999</optimize_decimation>
    <optimize_end_reg>1</optimize_end_reg>
    <optimize_iters>1000</optimize_iters>
    <optimize_maxAngle>60</optimize_maxAngle>
    <optimize_particles>256</optimize_particles>
    <optimize_procrustes_interval>1</optimize_procrustes_interval>
    <optimize_start_reg>10</optimize_start_reg>
    <optimize_weight>5</optimize_weight>
    <parallel_enabled>true</parallel_enabled>
    <pca_range>2</pca_range>
    <pca_steps>20</pca_steps>
    <regression_steps>50</regression_steps>
    <smoothing_amount>0</smoothing_amount>
    <spacing>9</spacing>
    <tool_state>optimize</tool_state>
    <zoom_state>7</zoom_state>
    <cutPlanes_file></cutPlanes_file>
    <shapes>
        <shape id="0">
            <initial_mesh>C:/Users/kdear/Documents/Slicer/HumC.nrrd</initial_mesh>
            <groomed_mesh>C:/Users/kdear/Documents/Slicer/HumC_DT.nrrd</groomed_mesh>
        </shape>
        <shape id="1">
            <initial_mesh>C:/Users/kdear/Documents/Slicer/HumA.nrrd</initial_mesh>
            <groomed_mesh>C:/Users/kdear/Documents/Slicer/HumA_DT.nrrd</groomed_mesh>
        </shape>
        <shape id="2">
            <initial_mesh>C:/Users/kdear/Documents/Slicer/HumB.nrrd</initial_mesh>
            <groomed_mesh>C:/Users/kdear/Documents/Slicer/HumB_DT.nrrd</groomed_mesh>
        </shape>
    </shapes>
</project>

Attachment: HumHeads.zip
Description: Zip compressed data


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