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Re: [shapeworks-users] ShapeWorks Release and Meeting Slides


Chronological Thread 
  • From: Shireen Elhabian <shireen@sci.utah.edu>
  • To: Steven A <stevenagl12@gmail.com>
  • Cc: Shireen Elhabian <shireen@sci.utah.edu>, shapeworks-users@sci.utah.edu
  • Subject: Re: [shapeworks-users] ShapeWorks Release and Meeting Slides
  • Date: Fri, 8 Nov 2019 07:28:09 -0700
Hi Steven,

In the slides, we show two use cases demonstrating shape modeling workflows using two different types of user inputs (femurs for surface meshes and left atrium for segmentation - binary label maps). As you already have binary segmentations, I would either consider Studio that directly takes in segmentations or the python script for left atrium use case.

On choosing parameters, currently, most of the parameter selection (in the groom and optimize stages) rely on quality controlling your shapes after each step. For instance, in Studio, if you have shapes with fine anatomical details and you use smoothing (blurring) with relatively larger sigma and/or more iterations, these details will disappear, so you would decrease the sigma.

We are working on documenting some guidelines for parameter selection at different stages and it will be announced on the list. Meanwhile, please send us specific questions about running your data and we are more than happy to help you out.


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
Home Page: http://www.sci.utah.edu/~shireen

On Nov 8, 2019, at 7:07 AM, Steven A <stevenagl12@gmail.com> wrote:

I'm confused by the slides, how do you know what parameters to use for your meshes during the cleaning and optimization step? I'm trying to work with the kidney from binary labelmaps but there's no good directions for how it can be done...

On Thu, Nov 7, 2019, 21:53 Shireen Elhabian <shireen@sci.utah.edu> wrote:
Dear all,

Thanks for joining our monthly meeting today and looking forward to our next meeting in December. Meanwhile, please try out the latest release of ShapeWorks on your data and don’t hesitate to send us your questions, feedback, and/or feature requests. 

For your convenience, here is the link for today’s meeting slides.

You can find the latest release here:

The link for ShapeWorks data portal:

For questions, comments, feature requests, and feedback: Please feel free to use our Gitter forum (https://gitter.im/ShapeWorks) and/or our emailing list shapeworks-users@sci.utah.edu 

See (or talk to) you all next month with more interesting ShapeWorks updates!

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
Home Page: http://www.sci.utah.edu/~shireen



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