# Lung lesion segmentation

**URL:** <https://discourse.slicer.org/t/lung-lesion-segmentation/21967>\
**Category:** SlicerCIP\
**Created:** [February 14, 2022, 8:55pm UTC](https://discourse.slicer.org/t/lung-lesion-segmentation/21967 "2022-02-14T20:55:14Z")\
**Posts on this page:** 16\
**Page:** 1

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**Author:** ![Alexander\_The\_Great](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/alexander_the_great/32/14290_2.png) [@Alexander\_The\_Great](https://discourse.slicer.org/u/Alexander_The_Great)\
**Post date:** [February 14, 2022, 8:55pm UTC](https://discourse.slicer.org/t/lung-lesion-segmentation/21967/1 "2022-02-14T20:55:14Z")

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Hey. I am new to slicer segmentation. I try to segment lung nodules with the help of CIP lesion analyser, but unfortunately after the first successful nodule segmentation, I select the second nodule but I am unable to proceed with the segmentation button. Is there any way around? It is very useful in order to do a semi-automatic segmentation like that.

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/4/b/4bf83102b7245a77cfc7c360c650998c01f0a607.png)

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**Author:** ![rbumm](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/rbumm/32/9404_2.png) [@rbumm](https://discourse.slicer.org/u/rbumm)\
**Post date:** [February 14, 2022, 9:49pm UTC](https://discourse.slicer.org/t/lung-lesion-segmentation/21967/2 "2022-02-14T21:49:35Z")

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Hi,  
This seems to be an outdated module that needs servicing.  
I can not get it running either even not in 4.10.2  
Please describe what you would expect to have in your clinical workflow.  
I am not the creator of that package.  
Best regards  
rudolf

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**Author:** ![rbumm](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/rbumm/32/9404_2.png) [@rbumm](https://discourse.slicer.org/u/rbumm)\
**Post date:** [February 15, 2022, 11:13am UTC](https://discourse.slicer.org/t/lung-lesion-segmentation/21967/3 "2022-02-15T11:13:31Z")

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In the meantime, you could try to use the “Local threshold” effect of the “Segment Editor” with the following parameters:

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/7/0/700d6598159c64f5c2c15f524b6444a4032514f5.jpeg)

CTRL+left click into the nodule you want to segment - done.  
Please use Slicer preview 4.13. You need to install “Segment Editor Extra Effects” to have that effect available.

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**Author:** ![Alexander\_The\_Great](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/alexander_the_great/32/14290_2.png) [@Alexander\_The\_Great](https://discourse.slicer.org/u/Alexander_The_Great)\
**Post date:** [February 20, 2022, 1:17pm UTC](https://discourse.slicer.org/t/lung-lesion-segmentation/21967/4 "2022-02-20T13:17:24Z")

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Thank you so much for the help. I used the CIP plug-in as it seemed more specific to lung nodule analysis. I will try your suggested method. I will use the MIP viewer from CIP extension and segment the nodules as you suggested. Tried installing the “segment editor extra effects” with no luck. I will use the latest slicer preview and try again.  
Thanks again for your help

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**Author:** ![Alexander\_The\_Great](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/alexander_the_great/32/14290_2.png) [@Alexander\_The\_Great](https://discourse.slicer.org/u/Alexander_The_Great)\
**Post date:** [February 20, 2022, 2:53pm UTC](https://discourse.slicer.org/t/lung-lesion-segmentation/21967/5 "2022-02-20T14:53:55Z")

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Tried a lot of tricks in order to instal the “segment editor extra effects”. Just couldn’t. Could you please suggest a way? Thanks in advance.

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**Author:** ![rbumm](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/rbumm/32/9404_2.png) [@rbumm](https://discourse.slicer.org/u/rbumm)\
**Post date:** [February 21, 2022, 9:46am UTC](https://discourse.slicer.org/t/lung-lesion-segmentation/21967/6 "2022-02-21T09:46:08Z")

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> [@Alexander\_The\_Great](#):
>
> Could you please suggest a way?

Install Slicer 4.13. (important)

Go extension manager:

![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/1/1/11ffb2598710623e6a80064763dc43c39e0e5abd.png)

Enter “extra” in the input box at the upper right edge of the window:

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/1/f/1f8d07975528f425b4e318673992a490404ecab3.jpeg)

Install and restart Slicer.

After that, you should find “Local threshold” in the Segment Editor.

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<div class="post-metadata">

**Author:** ![Alexander\_The\_Great](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/alexander_the_great/32/14290_2.png) [@Alexander\_The\_Great](https://discourse.slicer.org/u/Alexander_The_Great)\
**Post date:** [February 22, 2022, 7:22pm UTC](https://discourse.slicer.org/t/lung-lesion-segmentation/21967/7 "2022-02-22T19:22:12Z")

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I am grateful to you for your guidance. Followed your screenshots and installed the extra effects extension. However, I don’t think I can do the segmentation. I followed the instructions but when I ctlr + left click, the whole are of the image flashes and I cannot continue with the segmentation. Are there some additional options I need to select?  
Thanks again for the help

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**Author:** ![rbumm](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/rbumm/32/9404_2.png) [@rbumm](https://discourse.slicer.org/u/rbumm)\
**Post date:** [February 22, 2022, 7:58pm UTC](https://discourse.slicer.org/t/lung-lesion-segmentation/21967/8 "2022-02-22T19:58:26Z")

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I produced a short clip, hope that helps.

[![](https://img.youtube.com/vi/NmG16cSwUHg/maxresdefault.jpg "Segmenting a lung nodule with 3D Slicer and "Local Threshold"") ](https://www.youtube.com/watch?v=NmG16cSwUHg)

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**Author:** ![Alexander\_The\_Great](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/alexander_the_great/32/14290_2.png) [@Alexander\_The\_Great](https://discourse.slicer.org/u/Alexander_The_Great)\
**Post date:** [February 22, 2022, 8:36pm UTC](https://discourse.slicer.org/t/lung-lesion-segmentation/21967/9 "2022-02-22T20:36:48Z")

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Did exactly what you didi but the nodule just doesn’t want to get segmentated. I add a video of my try.

[https://youtu.be/uXjJVoOIJyk](https://youtu.be/uXjJVoOIJyk)

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<div class="post-metadata">

**Author:** ![rbumm](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/rbumm/32/9404_2.png) [@rbumm](https://discourse.slicer.org/u/rbumm)\
**Post date:** [February 22, 2022, 8:41pm UTC](https://discourse.slicer.org/t/lung-lesion-segmentation/21967/10 "2022-02-22T20:41:08Z")

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You are using “Watershed” in your Local threshold dropdown field, I am using “GrowCut”

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<div class="post-metadata">

**Author:** ![Alexander\_The\_Great](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/alexander_the_great/32/14290_2.png) [@Alexander\_The\_Great](https://discourse.slicer.org/u/Alexander_The_Great)\
**Post date:** [February 23, 2022, 5:24pm UTC](https://discourse.slicer.org/t/lung-lesion-segmentation/21967/11 "2022-02-23T17:24:03Z")

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I did it with grow cut. The output is the same as I presented in the video

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<div class="post-metadata">

**Author:** ![rbumm](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/rbumm/32/9404_2.png) [@rbumm](https://discourse.slicer.org/u/rbumm)\
**Post date:** [February 23, 2022, 6:55pm UTC](https://discourse.slicer.org/t/lung-lesion-segmentation/21967/12 "2022-02-23T18:55:44Z")

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Are you able to share an anonymized dataset?

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<div class="post-metadata">

**Author:** ![Luis\_Santos](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/luis_santos/32/14428_2.png) [@Luis\_Santos](https://discourse.slicer.org/u/Luis_Santos)\
**Post date:** [February 24, 2022, 3:06am UTC](https://discourse.slicer.org/t/lung-lesion-segmentation/21967/13 "2022-02-24T03:06:22Z")

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Try to use grow from seeds.

[![](https://img.youtube.com/vi/R-lBsqAvSTA/maxresdefault.jpg "3D Slicer Tutorial #3: Scissors. Grow from seeds.") ](https://www.youtube.com/watch?v=R-lBsqAvSTA)

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<div class="post-metadata">

**Author:** ![rbumm](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/rbumm/32/9404_2.png) [@rbumm](https://discourse.slicer.org/u/rbumm)\
**Post date:** [February 24, 2022, 7:44am UTC](https://discourse.slicer.org/t/lung-lesion-segmentation/21967/14 "2022-02-24T07:44:32Z")

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> [@Alexander\_The\_Great](#):
>
> Did exactly what you did

Please try to adjust the “Local threshold” threshold slider in a way that the nodule gets completely filled, even gets a bit “overfilled”. Then CTRL+Left Click into the nodule again.

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/b/4/b40214fa4eda4093a9bd92bfb792db43226e1911.jpeg)

Make sure that “Editable intensity range” is unchecked.

![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/4/e/4e62e2e4086d1baacfeaef12658ae15f87b6114e.png)

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<div class="post-metadata">

**Author:** ![Alexander\_The\_Great](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/alexander_the_great/32/14290_2.png) [@Alexander\_The\_Great](https://discourse.slicer.org/u/Alexander_The_Great)\
**Post date:** [March 1, 2022, 11:04am UTC](https://discourse.slicer.org/t/lung-lesion-segmentation/21967/15 "2022-03-01T11:04:46Z")

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sorry to bother you again, but unfortunately I couldn’t manage to do it. Tried everything you said, experimented with other suggestions found online, but I couldn’t.  
The CIP plugin is a more user friendly way of doing the segmentations. Is there a way to install an older version of Slicer 3D that worked well with that?

Thanks in advance

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<div class="post-metadata">

**Author:** ![rbumm](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/rbumm/32/9404_2.png) [@rbumm](https://discourse.slicer.org/u/rbumm)\
**Post date:** [March 1, 2022, 12:58pm UTC](https://discourse.slicer.org/t/lung-lesion-segmentation/21967/16 "2022-03-01T12:58:05Z")

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No, I am not aware of such a version.  
The Slicer version that is recommended on the Chest Imaging Platform homepage and linked there for download does not include a fully working Lung Lesion Analyzer extension. I am not prepared to go further back in time for testing.