# Axial slides missing

**URL:** <https://discourse.slicer.org/t/axial-slides-missing/21918>\
**Category:** Support\
**Tags:** segmentation, views\
**Created:** [February 11, 2022, 3:01pm UTC](https://discourse.slicer.org/t/axial-slides-missing/21918 "2022-02-11T15:01:02Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![HodaGH](https://avatars.discourse-cdn.com/v4/letter/h/858c86/32.png) [@HodaGH](https://discourse.slicer.org/u/HodaGH)\
**Post date:** [February 11, 2022, 3:01pm UTC](https://discourse.slicer.org/t/axial-slides-missing/21918/1 "2022-02-11T15:01:02Z")

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Hi,

I have .AIM files of murine caudal vasculature from Scanco micro-CT which I opened with imagej , changed it to .NRRD and was able to open it in Slicer based on [this](https://discourse.slicer.org/t/support-for-aim-isq-files-generated-on-scanco-microct/6261) discussion. The image looks ok in imagej and also opened it with python scripts so no problem with my image but when I load it in Slicer some of the axial slides are missing. Is there any way to solve this? If not is there any way to connect the pieces in my segmentation?

 ![Screen Shot 2022-02-11 at 9.45.38 AM](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/c/9/c9864da484089a5f998c6c0ff9dc29e0282b0eff.jpeg)

Thank you,  
Hoda

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [February 11, 2022, 3:58pm UTC](https://discourse.slicer.org/t/axial-slides-missing/21918/2 "2022-02-11T15:58:18Z")

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Could you share the files (upload the files to dropbox, onedrive, google drive, etc. and post the link) so that we can have a look?

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<div class="post-metadata">

**Author:** ![HodaGH](https://avatars.discourse-cdn.com/v4/letter/h/858c86/32.png) [@HodaGH](https://discourse.slicer.org/u/HodaGH)\
**Post date:** [February 11, 2022, 4:58pm UTC](https://discourse.slicer.org/t/axial-slides-missing/21918/3 "2022-02-11T16:58:09Z")

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here you go [vasculature.nrrd - Google Drive](https://drive.google.com/file/d/1KPvXHoVtLgjGGCIGDfTRnVDIneYlxlmB/view?usp=sharing)

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<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [February 11, 2022, 7:27pm UTC](https://discourse.slicer.org/t/axial-slides-missing/21918/4 "2022-02-11T19:27:52Z")

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Thank you, in this reconstructed file there are indeed two dark regions. Could you please upload the input files (before reconstruction) so that we can see why the gaps are there?

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<div class="post-metadata">

**Author:** ![HodaGH](https://avatars.discourse-cdn.com/v4/letter/h/858c86/32.png) [@HodaGH](https://discourse.slicer.org/u/HodaGH)\
**Post date:** [February 13, 2022, 4:13am UTC](https://discourse.slicer.org/t/axial-slides-missing/21918/5 "2022-02-13T04:13:39Z")

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Thank you I see them now. I’ll ask if I can have them but is it possible to have a connected segmentation with these missing slides?  
I followed the vesselness instructions, created a seed fiducial then preview and start. then used thresholding in segment editor (also adjusted window level in the volume module ) but the three major vessels got segmented like this

 ![Screen Shot 2022-02-12 at 11.02.25 PM](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/3/d/3d30c4c4cbf1a8c2c48c2f38628eae70b4ff3049.png)  
how can I improve?

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<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [March 13, 2022, 5:00am UTC](https://discourse.slicer.org/t/axial-slides-missing/21918/6 "2022-03-13T05:00:09Z")

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This looks quite good. You can remove the noise using “Islands” effect and may further improve results using “Smoothing” effect.

You can also try using “Grow from seeds”, “Local threshold”, and “Fast marching” effects (in SegmentEditorExtraEffects extension) instead of simple “Threshold” effect for higher quality segmentation.