# Changing slice thickness for epicardial adipose tissue analysis

**URL:** <https://discourse.slicer.org/t/changing-slice-thickness-for-epicardial-adipose-tissue-analysis/16928>\
**Category:** Support\
**Created:** [April 2, 2021, 4:16pm UTC](https://discourse.slicer.org/t/changing-slice-thickness-for-epicardial-adipose-tissue-analysis/16928 "2021-04-02T16:16:16Z")\
**Posts on this page:** 7\
**Page:** 1

<div class="post-metadata">

**Author:** ![Mark\_Brahier](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/mark_brahier/32/5934_2.png) [@Mark\_Brahier](https://discourse.slicer.org/u/Mark_Brahier)\
**Post date:** [April 2, 2021, 4:16pm UTC](https://discourse.slicer.org/t/changing-slice-thickness-for-epicardial-adipose-tissue-analysis/16928/1 "2021-04-02T16:16:16Z")

</div>

I’m currently using 3D Slicer for manual segmentation of cardiac CTs to quantify epicardial adipose tissue. The CTs that I have are high resolution at a slice thickness of 0.5mm or less (some as small as 0.15mm). Within 3D Slicer, is there a way to “merge” segments so that the thickness is only 1mm (or perhaps even 2mm?). I know this will diminish the accuracy of the measurements to some extent, but it may be worth it to us for the time saved in analysis. I appreciate any advice on how to do this.

---

<div class="post-metadata">

**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [April 2, 2021, 4:19pm UTC](https://discourse.slicer.org/t/changing-slice-thickness-for-epicardial-adipose-tissue-analysis/16928/2 "2021-04-02T16:19:08Z")

</div>

Yes, you can set the geometry of the segmentation independent of the background (it’s set to the background by default). Use the segmentation geometry button next to the master volume selector.

[https://slicer.readthedocs.io/en/latest/user\_guide/image\_segmentation.html#basic-concepts](https://slicer.readthedocs.io/en/latest/user_guide/image_segmentation.html#basic-concepts)

---

<div class="post-metadata">

**Author:** ![Mark\_Brahier](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/mark_brahier/32/5934_2.png) [@Mark\_Brahier](https://discourse.slicer.org/u/Mark_Brahier)\
**Post date:** [April 2, 2021, 6:14pm UTC](https://discourse.slicer.org/t/changing-slice-thickness-for-epicardial-adipose-tissue-analysis/16928/3 "2021-04-02T18:14:31Z")

</div>

Thank you for this quick reply. Would you be able to provide additional details of where I need to go to adjust slice thickness? I apologize in advance, but I’m a novice at this and would appreciate any additional information. I’m using the latest version of Slicer.

---

<div class="post-metadata">

**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [April 2, 2021, 9:58pm UTC](https://discourse.slicer.org/t/changing-slice-thickness-for-epicardial-adipose-tissue-analysis/16928/4 "2021-04-02T21:58:42Z")

</div>

Hmm, good question. I thought you could just edit this in the segmentation geometry dialog, but I can’t seem to enable that mode easily. @lassoan or others?

---

<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:** [April 3, 2021, 12:21am UTC](https://discourse.slicer.org/t/changing-slice-thickness-for-epicardial-adipose-tissue-analysis/16928/5 "2021-04-03T00:21:11Z")

</div>

You may also choose to segment just 1 out of every 5-10 slices and use “Fill between slices” effect to create a full, high-resolution segmentation by smoothly interpolating between the segmented slices. You can insert additional slices anywhere where you find that the interpolated segmentation is not accurate enough.

---

<div class="post-metadata">

**Author:** ![Mark\_Brahier](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/mark_brahier/32/5934_2.png) [@Mark\_Brahier](https://discourse.slicer.org/u/Mark_Brahier)\
**Post date:** [April 3, 2021, 6:42pm UTC](https://discourse.slicer.org/t/changing-slice-thickness-for-epicardial-adipose-tissue-analysis/16928/6 "2021-04-03T18:42:39Z")

</div>

Thank you both, this is a great option. The issue I am running into now is that after “filling between slices,” the quantification of adipose tissue volume appears to be a lot lower than I would expect, approximately by a factor of 10. Because I manually segmented every 10th slice, I am wondering if the quantification is not capturing the slices that were segmented using the “fill between slices” feature. Is there a setting that I need to change?

---

<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:** [April 3, 2021, 9:37pm UTC](https://discourse.slicer.org/t/changing-slice-thickness-for-epicardial-adipose-tissue-analysis/16928/7 "2021-04-03T21:37:27Z")

</div>

> [@Mark\_Brahier](#):
>
> quantification of adipose tissue volume appears to be a lot lower than I would expect

It seems that you have not clicked “Apply” in “Fill between slices” effect to write the preview of interpolation results into the segmentation.