shapeworks-users

Text archives Help


Re: [shapeworks-users] Requesting assistance with ShapeWorks Optimization Step


Chronological Thread 
  • From: Shireen Elhabian <shireen@sci.utah.edu>
  • To: Alan Morris <amorris@sci.utah.edu>, shapeworks-users@sci.utah.edu
  • Cc: Shireen Elhabian <shireen@sci.utah.edu>
  • Subject: Re: [shapeworks-users] Requesting assistance with ShapeWorks Optimization Step
  • Date: Mon, 6 Jan 2020 15:13:34 -0700

Thanks Alan! Forwarding this to the users email list in case anyone has the same problem. We are working on a fix on our side.

Happy new year to all Shapeworks-users!

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 Jan 6, 2020, at 2:40 PM, Alan Morris <amorris@sci.utah.edu> wrote:

FYI...

---------- Forwarded message ---------
From: Kayley Dear <kayleyd5@gmail.com>
Date: Mon, Jan 6, 2020 at 2:37 PM
Subject: Re: [shapeworks-users] Requesting assistance with ShapeWorks Optimization Step
To: Alan Morris <amorris@sci.utah.edu>


Hi Alan,

I just realized in my excitement of getting this to work I forgot to hit send on my response! 

Thank you so much! This solved all the issues and I was able to confirm a measurable variable in morphology that we suspected played a role in impingement.

Thanks again and Happy New Year!

Kayley

On Thu, Dec 5, 2019 at 2:47 PM Alan Morris <amorris@sci.utah.edu> wrote:
Hi Kayley,

The problem you are running into is that the ShapeWorks tools do not currently support LPI oriented image volumes.  Unfortunately many of them either don't work or crash.  We are working on fixing this, but for the time being you must reorient them to RAI.

Attached are your samples, reoriented in RAI.  I was able to load these in ShapeWorksStudio, groom and optimize with them with no problem.

To reorient image volumes, I would recommend using convert3d:


For example:

c3d HumA.nrrd -orient RAI -o HumA_RAI.nrrd

Thanks,
Alan



On Mon, Dec 2, 2019 at 2:49 PM Kayley Dear <kayleyd5@gmail.com> wrote:

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


-- 
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



  • Re: [shapeworks-users] Requesting assistance with ShapeWorks Optimization Step, Shireen Elhabian, 01/06/2020

Archive powered by MHonArc 2.6.18.

Top of page