Hi Alan,

 

Thank you for taking a look at the files.  Two of the feet do indeed have socks on, which will probably be the norm for most feet we will be looking at. The mean you show sure looks better than the blob we were getting before.

 

When do you think we can get a hold of ShapeWorksStudio (even in a beta form)?

 

We have a few Windows machines with 4 cores and 32 GB RAM so hopefully they will be able to run the models. Alternatively, what are the rules about getting a collaborator account to run jobs on a few nodes at SCI?  More importantly, is your latest version of Shapeworks compiled to run on any Unix systems?

 

Thanks,

Mike

 

From: Alan Morris [mailto:akenmorris@gmail.com]
Sent: Friday, October 24, 2014 2:29 PM
To: shapeworks-users@sci.utah.edu; Michael Harris
Cc: Joshua E Cates; Adam Cyr
Subject: Re: [shapeworks-users] Shapeworks 1.2 Win troubleshoot

 

Michael,

 

There are couple of bugs in the ShapeWorksGroom on the website that have been fixed since the last release.  Please download this zip file with newer executables for Windows:

 

http://www.sci.utah.edu/~amorris/for_michael_harris.zip

 

Also in the zip file are parameter files and the results of my running your data through ShapeWorksGroom and ShapeWorksRun and an analysis file for use with either ShapeWorksView or ShapeWorksView2.

 

I used:

 

ShapeWorksGroom groom.xml center auto_crop auto_pad antialias fastmarching blur

ShapeWorksRun optimize.xml

ShapeWorksView2 analysis.xml 

 

Both the ShapeWorksGroom and ShapeWorksRun steps require a huge amount of RAM for these large images (20GB or so, I think, though you might get away with 16GB).  The groom step took about an hour with a 4-core machine and the optimization took about 15 minutes.

 

I've also attached an image from our new tool, ShapeWorksStudio (still in development) showing all the initial data together.  It looks like two of the images are quite different than the other two.  Looks like they have socks on. :)

 

If you have any other questions, please let me know.

 

Thanks,

Alan

 

 

 

 

On Mon, Oct 20, 2014 at 4:26 PM, Michael Harris <Michael.D.Harris@du.edu> wrote:

Hey Josh,

 

As I mentioned a few weeks ago, we would like to try ShapeWorks for a SSM of the foot.  To start, we have been trying a set of four feet.

 

We have tried to run ShapeWorks in two ways:

1-      Using the Windows v1.2.0 available on the SCI website

2-      Using the protocol and Unix executables from the femur shape modeling paper I did with Manasi

 

We are having trouble running the software in each case.  On Windows, we have tried running with and without the Groom steps.  After ShapeWorksRun we get points files but they form shapes that are just a mess and not anything like the feet we input.  If we try to look at the individual samples in ShapeWorksView, the program either crashes or shows a mess of blocks that appear meaningless.

 

In Unix, I keep getting a ‘Segmentation fault’ when trying to run the particle initialization.  I have run the shapes through all the preprocessing steps that I used on the past, even the ones that are redundant with some of the preprocessing I do before ShapeWorks (e.g. aligning, trimming the bounding boxes, padding, filling holes, cutting out data that I don’t want to affect the shape analysis).

 

Attached is a folder with the 4 samples in nrrd format.  As input to ShapeWorks we have also tried mha and tiff,  but get the same results.    

 

Is it possible for you or one of your people to run this small sample set through ShapeWorks to see if you can get it to work?  If there are newer executables that would be better than what are on the website, we would be happy to try them ourselves.

 

Thanks,

Mike

______________________________

Michael D. Harris, PhD

Center for Orthopaedic Biomechanics

University of Denver

michael.d.harris@du.edu

www.du.edu/biomechanics