# How to threshold only one slice in the DICOM Module

**URL:** <https://discourse.slicer.org/t/how-to-threshold-only-one-slice-in-the-dicom-module/10602>\
**Category:** Support\
**Created:** [March 9, 2020, 7:42pm UTC](https://discourse.slicer.org/t/how-to-threshold-only-one-slice-in-the-dicom-module/10602 "2020-03-09T19:42:39Z")\
**Posts on this page:** 7\
**Page:** 1

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**Author:** ![Vincent\_C](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/vincent_c/32/5759_2.png) [@Vincent\_C](https://discourse.slicer.org/u/Vincent_C)\
**Post date:** [March 9, 2020, 7:42pm UTC](https://discourse.slicer.org/t/how-to-threshold-only-one-slice-in-the-dicom-module/10602/1 "2020-03-09T19:42:40Z")

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Hi all,

I have loaded a 3D- CT scan into Slicer using the DICOM module. How can I apply thresholding to only one slice?

Thanks

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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:** [March 9, 2020, 9:18pm UTC](https://discourse.slicer.org/t/how-to-threshold-only-one-slice-in-the-dicom-module/10602/2 "2020-03-09T21:18:28Z")

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There are many ways to do it. What would you like to achieve?

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**Author:** ![Vincent\_C](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/vincent_c/32/5759_2.png) [@Vincent\_C](https://discourse.slicer.org/u/Vincent_C)\
**Post date:** [March 9, 2020, 10:08pm UTC](https://discourse.slicer.org/t/how-to-threshold-only-one-slice-in-the-dicom-module/10602/3 "2020-03-09T22:08:10Z")

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Hi Andras,

Thanks for the reply. I want to achieve accurate segmentation of muscle, SAT and VAT of the entire thoracolumbar region from T1 - L5. The method I was planning was to threshold 17 mid-vertebra slices and manually correcting them, then using the Fill between slice effect to propagate to the other slices and finally manually correcting them again. Is this a solid method to achieve the highest accuracy segmentation for a high resolution CT-volume? I am open to other suggestions :).

Thanks

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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 9, 2020, 11:58pm UTC](https://discourse.slicer.org/t/how-to-threshold-only-one-slice-in-the-dicom-module/10602/4 "2020-03-09T23:58:39Z")

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Manual correction typically takes much longer time than specifying a region from scratch. So, I would definitely not recommend to create an initial “segmentation” with simple thresholding.

Instead, I would recommend to try these options:

- Paint effect with appropriate “Editable intensity range”. You can find the correct threshold range in Threshold effect and then click “Use for masking”.
- Draw effect, potentially with “Editable intensity range”.
- Level tracing effect.

You may try to pre-process the image to reduce noise and make regions more homogeneous. For example, try Anisotropic Diffusion filters (in Filtering / Denoising category), or various other filters in Simple Filters module.

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<div class="post-metadata">

**Author:** ![Vincent\_C](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/vincent_c/32/5759_2.png) [@Vincent\_C](https://discourse.slicer.org/u/Vincent_C)\
**Post date:** [March 10, 2020, 1:39am UTC](https://discourse.slicer.org/t/how-to-threshold-only-one-slice-in-the-dicom-module/10602/5 "2020-03-10T01:39:19Z")

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Great thanks for the suggestions! I still want to experiment thresholding at a single slice. You mentioned there are many ways to do this for a CT scan loaded using the DICOM module?

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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:** [March 10, 2020, 1:46am UTC](https://discourse.slicer.org/t/how-to-threshold-only-one-slice-in-the-dicom-module/10602/6 "2020-03-10T01:46:25Z")

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The easiest to see how bad the result is if you use simple thresholding is to threshold the entire volume, using Threshold effect. If you really want to threshold only a handful of slices, then you can set editable intensity range in Threshold effect, click Use for masking, then use Paint effect with a huge brush (so that you can easily cover the entire slice with a single click or a short paintstroke).

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<div class="post-metadata">

**Author:** ![Vincent\_C](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/vincent_c/32/5759_2.png) [@Vincent\_C](https://discourse.slicer.org/u/Vincent_C)\
**Post date:** [March 10, 2020, 3:18am UTC](https://discourse.slicer.org/t/how-to-threshold-only-one-slice-in-the-dicom-module/10602/7 "2020-03-10T03:18:04Z")

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Hi Andras,

Your fast responses are always much appreciated! Thanks.