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:

http://www.itksnap.org/pmwiki/pmwiki.php?n=Convert3D.Documentation

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

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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