Hi Alan,

Thanks a lot for your help! This feature is great and I have got some nice looking visualizations (shape mean and difference shown below). Can I ask a few more questions? Just curious about some finer adjustments.

1. Is there a way to get bigger arrows in the group difference visualization?

The arrows seem small and hard to see now. Perhaps this is just a result of too few particles.

2. Is there a way to adjust the color mapping in the group difference visualization?

It seem 0 is mapped to yellow in the current mapping. I think in our case it would be preferable to map it to black.

3. What could improve the optimization on very thin shapes?

It has some mismatching issues when the particle number is increased from 64 to 128 (shown below, figures from left to right show the deformation of the first principal component, mismatched areas are circled in orange).

Here are the original segmentation, groom parameters, groomed segmentation and optimization parameters:

Thank you!

Wenzheng

Hi Wenzheng,

Yes, this functionality is available in Studio, for example:

http://sciinstitute.github.io/ShapeWorks/latest/studio/studio-analyze.html#group

If you click the 'mean' for each group, you can export the reconstructed mesh from the File->Export menu.

Let me know if you have further questions.

Thanks,

Alan

On 8/1/22, 5:15 PM, "shapeworks-users-request@sci.utah.edu on behalf of wenzheng tao" <shapeworks-users-request@sci.utah.edu on behalf of wztao@cs.utah.edu> wrote:

    Hello,

    I am using Shapeworks to do shape analysis on some soft tissues and I

    would like to visualize the group difference in a way similar to the

    attached "norm_vec.png". It is a figure from [1], just as an example. I

    am wondering if Shapeworks has built in functions that can help me

    achieve the goals and I think there are mainly 2 questions.

    1. Is there a way to get a nice mean mesh for a subgroup?

    I assume it needs these steps: export the mean mesh from Shapeworks

    Studio, average the particles of the subjects in a selected group, warp

    the mean mesh to match the average particles. Does Shapeworks have these

    functions (I can do the averaging in Python)?

    2. Can shapeworks visualize normal vectors with colored arrows?

    I'd like to get a similar figure like the attached "norm_vec.png".

    Thanks for your help!

    Wenzhneg

    Ref:

    [1] Cates, Joshua, Lisa Nevell, Suresh I. Prajapati, Laura D. Nelon,

    Jerry Y. Chang, Matthew E. Randolph, Bernard Wood, Charles Keller, and

    Ross T. Whitaker. "Shape analysis of the basioccipital bone in

    Pax7-deficient mice." Scientific reports 7, no. 1 (2017): 1-10.