# LungCTAnalyzer extension for lung CT segmentation and analysis for COVID-19 assessment

**URL:** <https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006>\
**Category:** Support\
**Tags:** feature, lungctanalyzer\
**Created:** [December 11, 2020, 5:33pm UTC](https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006 "2020-12-11T17:33:10Z")\
**Posts on this page:** 17\
**Page:** 3

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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:** [May 1, 2022, 6:20pm UTC](https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006/41 "2022-05-01T18:20:49Z")

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I can not yet reproduce your black preview in 3D, mine (in Slicer 4.13 and LCTA 2.47) is colored.

Anyway, if you **enabled** the 3D **preview** , you should “ **Hide preview** in 3D” afterwards to obtain only the final output segmentation in the 3D view.

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/8/c/8c0aff6f6c53386904b361205612572e2058cafb.png)

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**Author:** ![Aaron\_Tsai](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/aaron_tsai/32/16949_2.png) [@Aaron\_Tsai](https://discourse.slicer.org/u/Aaron_Tsai)\
**Post date:** [October 15, 2022, 7:25am UTC](https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006/42 "2022-10-15T07:25:28Z")

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Hi Rudolf,

I would like to test the package on rodents’ lung tissue analysis.  
When I move to step 2, that is the step I would need to place a few seeds.  
However, the image is kind of resample to very large voxels makes the images blurred.  
Dose this package only good for human CT images?  
Thank you very much,

Regards,  
Aaron

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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:** [October 15, 2022, 10:40am UTC](https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006/43 "2022-10-15T10:40:22Z")

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Hi,  
The package has been developed for human CT and the Lung CT Segmenter module does not yet work reliably with Micro CT. However, you could go to “Segment Editor”, and create a “lung segmentation” with “right lung” and “left lung” by using the “Grow From Seeds” effect. As soon as you have good lung masks you could then run the “Lung CT Analyzer” module and use the “lung segmentation” with the lung masks as input segmentation.  
Regards  
Rudolf

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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:** [October 15, 2022, 1:11pm UTC](https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006/44 "2022-10-15T13:11:19Z")

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I think the only value hardcoded for human clinical CT is the preview image resolution of 2mm. This is probably too large for microCT.

You can easily modify this value by editing this line in LungCTSegmenter.py file:

> <https://github.com/rbumm/SlicerLungCTAnalyzer/blob/0ebbfee16245c44c5f2b3e848f93eb3e045ee6dc/LungCTSegmenter/LungCTSegmenter.py#L924>

Alternatively, you can modify the spacing value of the volume in Volumes module to be 10x larger. This does not change the image in any way, it just makes all length measurements 10x larger.

@rbumm we could consider allowing users to edit this value in some advanced parameters section in the GUI.

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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:** [October 15, 2022, 2:36pm UTC](https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006/45 "2022-10-15T14:36:32Z")

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@lassoan never thought you could set volume spacing from the Volumes extension directly.  
So now I can confirm that setting a rodent microCT´s spacing from 0.133mm 10 x larger enables the use of Lung CT Segmenter

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/a/e/ae4e1422cf4abb20f0c079c030e5b49ce81fbf4e.jpeg)

with the following lung thresholds:  
 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/b/f/bfad1c5a8a395fe89b5c39f278873523cf790617.png)

The other option does not work for me yet. Testing …

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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:** [October 15, 2022, 3:09pm UTC](https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006/46 "2022-10-15T15:09:19Z")

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> [@lassoan](#):
>
> ```auto
> parameters = {"outputPixelSpacing": "2.0,2.0,2.0", "InputVolume": self.inputVolume, "interpolationType": "linear", "OutputVolume": self.resampledVolume}
> 
> ```

To my understanding setting

```auto
914. parameters = {"outputPixelSpacing": "0.,0.,0.", "InputVolume": self.inputVolume, "interpolationType": "linear", "OutputVolume": self.resampledVolume}

```

should leave the spacing untouched in resampling, 2D views are not blurred, but the lung preview looks like this:

![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/1/a/1aa506eee94471873748daeed399cc4bdc6dd9af.jpeg)

… and “Apply” hangs Slicer.

Any ideas?

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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:** [October 15, 2022, 5:10pm UTC](https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006/47 "2022-10-15T17:10:12Z")

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0 spacing is invalid, do not set that value. If you don’t resample then computation time will be too long for interactive use. If you do not want to expose spacing as a parameter to the users (because it is too technical) then we could add a “lung size” (diameter of the lungs along a chosen anatomical axis) and compute the spacing relative to that. It is important that this spacing is not related to the input image resolution but the level of detail that we want for the segmentation preview.

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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:** [October 15, 2022, 7:54pm UTC](https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006/48 "2022-10-15T19:54:46Z")

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Setting spacing directly to 1 mm (original 0.188mm) and then using 2.0, 2.0, 2.0 works well. What would be your suggestion for a corresponding ouputPixelSpacing setting to achieve a similar result by leaving the input spacing at 0.188mm?

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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:** [October 16, 2022, 1:55am UTC](https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006/49 "2022-10-16T01:55:17Z")

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If you had to increase the spacing of the original image by approximately 5x (from 0.188mm to 1mm) then it means that you could instead decrease the spacing of the preview image by approximately 5x to have about the same level of detail. So, instead of 2.0mm spacing, use **0.4mm** spacing for the preview image.

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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:** [October 16, 2022, 7:41am UTC](https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006/50 "2022-10-16T07:41:42Z")

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Yes, but it does not work for some reason. I will open an issue and we can discuss it there.

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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:** [November 27, 2022, 8:23pm UTC](https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006/51 "2022-11-27T20:23:45Z")

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Split this topic on November 27, 2022, 8:23pm UTC

2 posts were split to a new topic: [LungCTAnalyzer extension used for research paper](https://discourse.slicer.org/t/lungctanalyzer-extension-used-for-research-paper/26466)

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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:** [September 23, 2024, 1:38am UTC](https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006/52 "2024-09-23T01:38:08Z")

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Split this topic on September 23, 2024, 1:38am UTC

A post was split to a new topic: [LungCTAnalyzer for pneumonia + pleural effusion cases](https://discourse.slicer.org/t/lungctanalyzer-for-pneumonia-pleural-effusion-cases/38490)

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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:** [September 23, 2024, 1:25am UTC](https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006/53 "2024-09-23T01:25:46Z")

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Split this topic on September 23, 2024, 1:25am UTC

A post was split to a new topic: [Lung volume measurement](https://discourse.slicer.org/t/lung-volume-measurement/38489)

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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:** [September 25, 2024, 7:53pm UTC](https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006/54 "2024-09-25T19:53:51Z")

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Split this topic on September 25, 2024, 7:53pm UTC

2 posts were split to a new topic: [Lung lobe input segment is missing](https://discourse.slicer.org/t/lung-lobe-input-segment-is-missing/38540)

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**Author:** ![yayale](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/yayale/32/79701_2.png) [@yayale](https://discourse.slicer.org/u/yayale)\
**Post date:** [April 7, 2025, 2:15pm UTC](https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006/55 "2025-04-07T14:15:57Z")

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Hello,

I am trying to make use of this extension. But the documentation is not enough to understand different values in the results table, and the color legend.  
Is there a clear document that explains the details of this extension ?

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**Author:** ![Vuk\_Vidic](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/vuk_vidic/32/81334_2.png) [@Vuk\_Vidic](https://discourse.slicer.org/u/Vuk_Vidic)\
**Post date:** [October 27, 2025, 10:57am UTC](https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006/56 "2025-10-27T10:57:14Z")

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Hello, i have a problem with Analyzer Results, in report Extended analysis (Table 2) all results are zero (0).

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<div class="post-metadata">

**Author:** ![yilinguo256](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/yilinguo256/32/82709_2.png) [@yilinguo256](https://discourse.slicer.org/u/yilinguo256)\
**Post date:** [August 12, 2026, 7:29am UTC](https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006/57 "2026-08-12T07:29:32Z")

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**Has the issue with the zero results been resolved? I’m facing this problem now. Thanks!**

[Previous page](https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006.md?page=2)