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Re: [shapeworks-users] problem with Shapeworks


Chronological Thread 
  • From: Shireen Elhabian <shireen@sci.utah.edu>
  • To: Feng Wei <fwei@g.clemson.edu>
  • Cc: shapeworks-users@sci.utah.edu, Shireen Elhabian <shireen@sci.utah.edu>
  • Subject: Re: [shapeworks-users] problem with Shapeworks
  • Date: Thu, 15 Feb 2018 08:48:12 -0700

Hi Feng,

There is a 3D procrustes alignment step that is performed within each optimization process depending on the current status of the corresponding particles. This alignment should factor out translation, rotation and scaling. In case you want to model scaling as a mode of variation, you could set this scaling off. 

However, if the input shapes are way out of alignment. This might cause some optimization issues. Typically, I would bring the shapes into a very rough alignment first before feeding them to shapeworks, for instance, aligning the shapes based on their center of mass. There are tools that might help you with this preprocessing step (e.g ANTs and elastix). Hope this helps ... 

thanks and best regards
Shireen


------------------------------------------
Shireen Elhabian, M.Sc., Ph.D.
Research Assistant Professor
School of Computing
Scientific Computing and Imaging Institute
University of Utah
WEB 2815
72 Central Campus Drive, Salt Lake City, UT, 84112
Phone (801) 587-3206
Fax (801) 585-6513




On Feb 15, 2018, at 8:41 AM, Feng Wei <fwei@g.clemson.edu> wrote:

Shireen,

  Thank you for the reply.

  I solved the bug. 


   One more question: Does this software do any alignment work? How did it do the 3D shape alignment?

Thanks,
Feng

On Thu, Feb 15, 2018 at 10:37 AM, Shireen Elhabian <shireen@sci.utah.edu> wrote:
Hi Feng,

This might be a memory problem. Are you having the same problem with the torus and ellipse datasets. I would try to use smaller number of shapes (may be three of them). I would also monitor the memory usage of your machine to see if it is peaking at some point prior to this error message.

thanks and best regards
Shireen


------------------------------------------
Shireen Elhabian, M.Sc., Ph.D.
Research Assistant Professor
School of Computing
Scientific Computing and Imaging Institute
University of Utah
WEB 2815
72 Central Campus Drive, Salt Lake City, UT, 84112
Phone (801) 587-3206
Fax (801) 585-6513




On Feb 15, 2018, at 7:58 AM, Feng Wei <fwei@g.clemson.edu> wrote:

Hi,

     I am testing the Shapeworks. I followed the exact steps listed on "https://github.com/SCIInstitute/ShapeWorksStudio/releases". I met the same problem with the provided examples in "femur.zip" every time when I clicked the "optimize" button.

     Please see the attached images for the problem.


Sincerely,
Feng


<image.png><image.png>




--
Feng Wei
Ph.D. Student
The Clemson-MUSC Joint Bioengineering Program
Address: 68 President Street BEB 221/223, Charleston, SC 29425
<image001.png>


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--
Feng Wei
Ph.D. Student
The Clemson-MUSC Joint Bioengineering Program
Address: 68 President Street BEB 221/223, Charleston, SC 29425
Phone: 843.876.2381 Cell: 843.303.8431
<image001.png>


This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error, please delete it from your computer. Under no circumstances are you permitted to save, copy, forward or otherwise disseminate the information contained in this email if you are not the intended recipient.




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