# Hollow Shape After Importing Data **URL:** \ **Category:** Uncategorized\ **Created:** [March 29, 2023, 7:15pm UTC](https://shapeworks.discourse.group/t/hollow-shape-after-importing-data/125 "2023-03-29T19:15:54Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![KristinBindas](https://avatars.discourse-cdn.com/v4/letter/k/65b543/32.png) [@KristinBindas](https://shapeworks.discourse.group/u/KristinBindas)\ **Post date:** [March 29, 2023, 7:15pm UTC](https://shapeworks.discourse.group/t/hollow-shape-after-importing-data/125/1 "2023-03-29T19:15:54Z")
Hi there everyone. I am having a problem with importing my nrrd file from 3D slicer to shape works. To gain the 3D model, i interpolated the shape using “fill between slices” tool, then used the threshold tool and smoothing tooth (Gaussian) to gain a smooth shape of the tibia. After exporting as an nrrd, the shape comes up as hollow. I provided a picture below. This hasn’t happened with me before. Any help is appreciated. ![image](https://global.discourse-cdn.com/free1/uploads/shapeworks/original/1X/407595b1334ab3a68ad5232c65b308677b51f768.jpeg) ---
**Author:** ![amorris](https://avatars.discourse-cdn.com/v4/letter/a/73ab20/32.png) [@amorris](https://shapeworks.discourse.group/u/amorris)\ **Post date:** [March 29, 2023, 9:40pm UTC](https://shapeworks.discourse.group/t/hollow-shape-after-importing-data/125/2 "2023-03-29T21:40:16Z")
Does your segmentation perhaps run to the end of the image on any side? If you enable padding with the groom step and run that, does it close? ---
**Author:** ![KristinBindas](https://avatars.discourse-cdn.com/v4/letter/k/65b543/32.png) [@KristinBindas](https://shapeworks.discourse.group/u/KristinBindas)\ **Post date:** [March 29, 2023, 10:59pm UTC](https://shapeworks.discourse.group/t/hollow-shape-after-importing-data/125/3 "2023-03-29T22:59:00Z")
Hi there, I’m not sure what you mean by run to the end of the image. I segmented each end, and the model shows up completely in slicer. I tried to use the groom step with padding and it gave me an error message and would not let me proceed. ---
**Author:** ![amorris](https://avatars.discourse-cdn.com/v4/letter/a/73ab20/32.png) [@amorris](https://shapeworks.discourse.group/u/amorris)\ **Post date:** [March 30, 2023, 12:56am UTC](https://shapeworks.discourse.group/t/hollow-shape-after-importing-data/125/4 "2023-03-30T00:56:26Z")
I mean that the segmentation goes to the edge of the image, like this: ![image](https://global.discourse-cdn.com/free1/uploads/shapeworks/original/1X/d9194de7ce62714b9b09d5de65d7c8cdaab5bd99.png) What was the error you received? Is there a chance you could share this NRRD file with me at amorris@sci.utah.edu? ---
**Author:** ![KristinBindas](https://avatars.discourse-cdn.com/v4/letter/k/65b543/32.png) [@KristinBindas](https://shapeworks.discourse.group/u/KristinBindas)\ **Post date:** [March 31, 2023, 12:50am UTC](https://shapeworks.discourse.group/t/hollow-shape-after-importing-data/125/5 "2023-03-31T00:50:06Z")
It does not go to the end of the image, as the bone does not take up the full image. I’ll attach a picture of what I mean below. The error I’m receiving is “mesh contained no points”. I’ll share the NRRD file in a separate email. ![Screen Shot 2023-03-30 at 8.49.23 PM.png](https://global.discourse-cdn.com/free1/uploads/shapeworks/original/1X/e2a6c1e43ec6554e114ab8a09662670255836969.png) ![Screen Shot 2023-03-30 at 8.47.13 PM.png](https://global.discourse-cdn.com/free1/uploads/shapeworks/original/1X/5d734d92e4e1e43779a8697892bfaf5de2312659.png) ---
**Author:** ![amorris](https://avatars.discourse-cdn.com/v4/letter/a/73ab20/32.png) [@amorris](https://shapeworks.discourse.group/u/amorris)\ **Post date:** [March 31, 2023, 6:42pm UTC](https://shapeworks.discourse.group/t/hollow-shape-after-importing-data/125/6 "2023-03-31T18:42:23Z")
Thanks for sending the image. So there are a few issues here. First, the segmentation does run to the end of the image, in the Z direction: ![image](https://global.discourse-cdn.com/free1/uploads/shapeworks/original/1X/060800b2cffed66a4ee31095ed9fd02caf31faa2.png) This is why it’s not capped at the top and bottom in your original image. This can be addressed with padding as I described. The message about not having any points is due to the image processing steps wiping out the entire segmentation. Unfortunately, the parameters for some filters are in world units. For example, a blur sigma of 2.0 is massive for an image with spacing that is 0.06 units. Unfortunately, the default parameters probably won’t work well for images with this small of units. Starting with just padding and DT: ![image](https://global.discourse-cdn.com/free1/uploads/shapeworks/original/1X/577adffe495354a0a295d90f3d0580b6d9ea4c96.jpeg) From there, you can experiment with adding other steps. I would recommend resampling to a larger spacing as you probably aren’t looking to model very tiny granularity on this surface. Here is a fairly smoothed one, for example: ![image](https://global.discourse-cdn.com/free1/uploads/shapeworks/original/1X/e1ed2890d5f580d768ae20c146be7572df5a9541.jpeg) It needed a significant amount of padding in order for the antialiasing and blurring to not run off the image. ---
**Author:** ![KristinBindas](https://avatars.discourse-cdn.com/v4/letter/k/65b543/32.png) [@KristinBindas](https://shapeworks.discourse.group/u/KristinBindas)\ **Post date:** [April 5, 2023, 4:19pm UTC](https://shapeworks.discourse.group/t/hollow-shape-after-importing-data/125/7 "2023-04-05T16:19:53Z")
Thank you so much for this. I was able to do this for most of my models with success. However, for one of my models I had to mirror my image before segmenting in order to properly compare the geometry. This nrrd file is giving me issues with the grooming step. I am able to complete the first groom with padding and DT (picture attached), but when I complete the second groom run into an issue (picture attached). Do you know how I could prevent this? ![Screen Shot 2023-04-05 at 12.11.21 PM](https://global.discourse-cdn.com/free1/uploads/shapeworks/original/1X/71d8761e0c2d9466770b45b908d8244640663010.jpeg) ![Screen Shot 2023-04-05 at 12.16.35 PM](https://global.discourse-cdn.com/free1/uploads/shapeworks/original/1X/5a4b3dba26132433d844b20e7bf5ac35142584d7.jpeg) ---
**Author:** ![amorris](https://avatars.discourse-cdn.com/v4/letter/a/73ab20/32.png) [@amorris](https://shapeworks.discourse.group/u/amorris)\ **Post date:** [April 6, 2023, 10:20pm UTC](https://shapeworks.discourse.group/t/hollow-shape-after-importing-data/125/8 "2023-04-06T22:20:46Z")
Can you send me this NRRD file? How are you mirroring it? You could also try the “Reflect” grooming option.