# Meniscus SSM Help **URL:** \ **Category:** Uncategorized\ **Created:** [August 31, 2025, 5:40pm UTC](https://shapeworks.discourse.group/t/meniscus-ssm-help/379 "2025-08-31T17:40:52Z")\ **Posts on this page:** 17\ **Page:** 1
**Author:** ![aceegreene](https://avatars.discourse-cdn.com/v4/letter/a/6f9a4e/32.png) [@aceegreene](https://shapeworks.discourse.group/u/aceegreene)\ **Post date:** [August 31, 2025, 5:40pm UTC](https://shapeworks.discourse.group/t/meniscus-ssm-help/379/1 "2025-08-31T17:40:52Z")
Hi everyone - I have segmented menisci for which I want to do SSM using Shapeworks however, I am having trouble getting good results post optimization where the images appear jagged/spiky. The results post grooming at least visually look fine. I have tried multiple iterations of grooming and optimization parameters and none of them really solve this issue. Attaching below the latest I tried including the original segmentations: ![Screenshot 2025-08-31 at 12.36.06 PM](https://global.discourse-cdn.com/free1/uploads/shapeworks/original/1X/07a566863dacb313905903a128f0159580cdb9a3.jpeg) Image: post optimization **I have tried all different kinds of methods with the optimization, lower particle counts from 64 onwards, adding/removing procrustes, increasing iterations, converting to meshes etc.** One thing that improves things but not good enough is increasing relative weighting but does not get desired results. So I am confused about next steps and unsure if it is a grooming problem or an optimization problem and how to proceed. Your help will be much appreciated! P.S. this is also just a test run with 6 later menisci. I have more data I can use in case that solves the problem. ---
**Author:** ![aceegreene](https://avatars.discourse-cdn.com/v4/letter/a/6f9a4e/32.png) [@aceegreene](https://shapeworks.discourse.group/u/aceegreene)\ **Post date:** [August 31, 2025, 5:42pm UTC](https://shapeworks.discourse.group/t/meniscus-ssm-help/379/2 "2025-08-31T17:42:10Z")
![Screenshot 2025-08-31 at 12.33.52 PM](https://global.discourse-cdn.com/free1/uploads/shapeworks/original/1X/53714979a4d571e6c3e2595b415d78972a95752e.jpeg) Image 1: originals with grooming settings ---
**Author:** ![aceegreene](https://avatars.discourse-cdn.com/v4/letter/a/6f9a4e/32.png) [@aceegreene](https://shapeworks.discourse.group/u/aceegreene)\ **Post date:** [August 31, 2025, 5:42pm UTC](https://shapeworks.discourse.group/t/meniscus-ssm-help/379/3 "2025-08-31T17:42:41Z")
![Screenshot 2025-08-31 at 12.35.09 PM](https://global.discourse-cdn.com/free1/uploads/shapeworks/original/1X/c8382c965897be91c5b1e7757c04247b5ac5a3c5.jpeg) Image 2: groomed images with optimization parameters ---
**Author:** ![amorris](https://avatars.discourse-cdn.com/v4/letter/a/73ab20/32.png) [@amorris](https://shapeworks.discourse.group/u/amorris)\ **Post date:** [September 2, 2025, 7:34am UTC](https://shapeworks.discourse.group/t/meniscus-ssm-help/379/4 "2025-09-02T07:34:58Z")
When you run this in Studio, do the particles spread out well in the initial splits (lower particle counts)? If not, I would try reducing the initial relative weighting (e.g 0.05). Also, increasing the optimization iterations will not generally help if the particles are not already in correspondence. You can see where before optimization by reducing the optimization iterations to 0. ---
**Author:** ![aceegreene](https://avatars.discourse-cdn.com/v4/letter/a/6f9a4e/32.png) [@aceegreene](https://shapeworks.discourse.group/u/aceegreene)\ **Post date:** [September 2, 2025, 6:52pm UTC](https://shapeworks.discourse.group/t/meniscus-ssm-help/379/5 "2025-09-02T18:52:44Z")
They do spread out well in the initial splits (I think), and I think correspondence isn’t bad across the menisci although it isn’t perfect either. Attaching an image of the particles at 32 particle count below with the remaining settings being the same during optimization. And also attaching two more below with everything else being the same at 32 particles and optimization iterations at 0 OR initial relative weighting at 0.05. ![Screenshot 2025-09-02 at 1.45.41 PM](https://global.discourse-cdn.com/free1/uploads/shapeworks/original/1X/796fb9d4631904c02fd68d346c5125f687b52856.jpeg) image 1: 32 particles everything else same Let me know what you think I should do next. Thank you! ---
**Author:** ![aceegreene](https://avatars.discourse-cdn.com/v4/letter/a/6f9a4e/32.png) [@aceegreene](https://shapeworks.discourse.group/u/aceegreene)\ **Post date:** [September 2, 2025, 6:53pm UTC](https://shapeworks.discourse.group/t/meniscus-ssm-help/379/6 "2025-09-02T18:53:20Z")
![Screenshot 2025-09-02 at 1.47.07 PM](https://global.discourse-cdn.com/free1/uploads/shapeworks/original/1X/9778b85294b91bf19bf280ff70a7a5a41e4a180b.jpeg) image 2: 32 particles everything else same except optimization iterations 0. ---
**Author:** ![aceegreene](https://avatars.discourse-cdn.com/v4/letter/a/6f9a4e/32.png) [@aceegreene](https://shapeworks.discourse.group/u/aceegreene)\ **Post date:** [September 2, 2025, 6:54pm UTC](https://shapeworks.discourse.group/t/meniscus-ssm-help/379/7 "2025-09-02T18:54:00Z")
![Screenshot 2025-09-02 at 1.50.20 PM](https://global.discourse-cdn.com/free1/uploads/shapeworks/original/1X/bc0a3fc85d701ad34476c46be8e18bbabcee3374.jpeg) image 3: 32 particles everything else same except initial relative weighting 0.05. ---
**Author:** ![amorris](https://avatars.discourse-cdn.com/v4/letter/a/73ab20/32.png) [@amorris](https://shapeworks.discourse.group/u/amorris)\ **Post date:** [September 2, 2025, 9:58pm UTC](https://shapeworks.discourse.group/t/meniscus-ssm-help/379/8 "2025-09-02T21:58:58Z")
Ok, if these are in good correspondence, then I would increase the particles and see where it is going wrong. ---
**Author:** ![aceegreene](https://avatars.discourse-cdn.com/v4/letter/a/6f9a4e/32.png) [@aceegreene](https://shapeworks.discourse.group/u/aceegreene)\ **Post date:** [September 3, 2025, 6:36am UTC](https://shapeworks.discourse.group/t/meniscus-ssm-help/379/9 "2025-09-03T06:36:33Z")
Increased particles to 64, 128 and 256 while keeping everything else the same. Unsure what I am looking for so would be grateful for your input! But the optimization results are not improving as can be seen: ![Screenshot 2025-09-03 at 1.34.28 AM](https://global.discourse-cdn.com/free1/uploads/shapeworks/original/1X/fb77fc363f2a2cad8170f4de6921925e25b96089.jpeg) image 1: 64 particles ![Screenshot 2025-09-03 at 1.29.42 AM](https://global.discourse-cdn.com/free1/uploads/shapeworks/original/1X/148118769863c84eaa5d192b9a37007bd324795e.jpeg) image 2: 128 particles ![Screenshot 2025-09-03 at 1.36.15 AM](https://global.discourse-cdn.com/free1/uploads/shapeworks/original/1X/f410692ce80042ab31d8d99fb44bacd4c4740768.jpeg) image 3: 256 particles One thing I did notice was that when I increased the relative weighting to a 100, the optimized shapes didn’t have these spikes/jagged edges but they seemed very similar to each other visually, so unsure if that is a valid result. The other thing is that the jaggedness decreases (doesn’t go away though) if I increase the optimization iterations but also unsure if that is a valid approach given that the 0 optimization iterations are not giving good results. Thanks again for your help! ---
**Author:** ![amorris](https://avatars.discourse-cdn.com/v4/letter/a/73ab20/32.png) [@amorris](https://shapeworks.discourse.group/u/amorris)\ **Post date:** [October 22, 2025, 6:04pm UTC](https://shapeworks.discourse.group/t/meniscus-ssm-help/379/10 "2025-10-22T18:04:59Z")
I think the next thing I would try is turning on “normals” in optimization and use a normals weight of perhaps 5. This may help the optimization in the later splits. ---
**Author:** ![aceegreene](https://avatars.discourse-cdn.com/v4/letter/a/6f9a4e/32.png) [@aceegreene](https://shapeworks.discourse.group/u/aceegreene)\ **Post date:** [October 28, 2025, 6:45pm UTC](https://shapeworks.discourse.group/t/meniscus-ssm-help/379/11 "2025-10-28T18:45:56Z")
Thank you for your response, I was able to generate a decent model based on these recommendations. I am now trying to compare two groups via the group particle p-values option and when I export the mesh or its scalars, I see 8700+ values in the csv whereas I used 512 particles for my SSM. Would you be able to explain what these mean? And how do I get p-values for the particles I am seeing visually in Studio? ---
**Author:** ![amorris](https://avatars.discourse-cdn.com/v4/letter/a/73ab20/32.png) [@amorris](https://shapeworks.discourse.group/u/amorris)\ **Post date:** [October 28, 2025, 8:04pm UTC](https://shapeworks.discourse.group/t/meniscus-ssm-help/379/12 "2025-10-28T20:04:15Z")
In addition to the “Export Current Mesh Scalars” option, there is another export option, “Export Current Particle Scalars”. This will have the 512 values you are looking for. If you are currently displaying the group p-values, then these values will be the p-values. ---
**Author:** ![aceegreene](https://avatars.discourse-cdn.com/v4/letter/a/6f9a4e/32.png) [@aceegreene](https://shapeworks.discourse.group/u/aceegreene)\ **Post date:** [October 29, 2025, 10:04pm UTC](https://shapeworks.discourse.group/t/meniscus-ssm-help/379/13 "2025-10-29T22:04:21Z")
Got it, thank you! These p-values represent the statistical significance of the groups being compared in the group tab right? ---
**Author:** ![amorris](https://avatars.discourse-cdn.com/v4/letter/a/73ab20/32.png) [@amorris](https://shapeworks.discourse.group/u/amorris)\ **Post date:** [November 3, 2025, 9:17pm UTC](https://shapeworks.discourse.group/t/meniscus-ssm-help/379/14 "2025-11-03T21:17:41Z")
Yes, that’s correct. ---
**Author:** ![aceegreene](https://avatars.discourse-cdn.com/v4/letter/a/6f9a4e/32.png) [@aceegreene](https://shapeworks.discourse.group/u/aceegreene)\ **Post date:** [November 13, 2025, 7:24pm UTC](https://shapeworks.discourse.group/t/meniscus-ssm-help/379/15 "2025-11-13T19:24:39Z")
Thank you! Is there a way to tell which particle number corresponds where on the visual figure? Or do we just approximate? ---
**Author:** ![amorris](https://avatars.discourse-cdn.com/v4/letter/a/73ab20/32.png) [@amorris](https://shapeworks.discourse.group/u/amorris)\ **Post date:** [November 14, 2025, 10:16pm UTC](https://shapeworks.discourse.group/t/meniscus-ssm-help/379/16 "2025-11-14T22:16:25Z")
You can identify any particle by hovering over it with the mouse and pressing the “1” key, this will highlight it in white and color the rest of the colors by the distance on the mean shape. The particle ID will be shown in the status bar. ![image](https://global.discourse-cdn.com/free1/uploads/shapeworks/original/1X/50812d8528375496cc01c466230160cbb51a9957.jpeg) ---
**Author:** ![aceegreene](https://avatars.discourse-cdn.com/v4/letter/a/6f9a4e/32.png) [@aceegreene](https://shapeworks.discourse.group/u/aceegreene)\ **Post date:** [November 17, 2025, 4:12pm UTC](https://shapeworks.discourse.group/t/meniscus-ssm-help/379/17 "2025-11-17T16:12:15Z")
That works, thank you!