# Covid lung radiomics feature extraction

**URL:** <https://discourse.slicer.org/t/covid-lung-radiomics-feature-extraction/26395>\
**Category:** Radiomics\
**Created:** [November 23, 2022, 7:16am UTC](https://discourse.slicer.org/t/covid-lung-radiomics-feature-extraction/26395 "2022-11-23T07:16:37Z")\
**Posts on this page:** 11\
**Page:** 1

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**Author:** ![Nima\_Yousefi](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/nima_yousefi/32/66845_2.png) [@Nima\_Yousefi](https://discourse.slicer.org/u/Nima_Yousefi)\
**Post date:** [November 23, 2022, 7:16am UTC](https://discourse.slicer.org/t/covid-lung-radiomics-feature-extraction/26395/1 "2022-11-23T07:16:37Z")

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Hello  
I’m working on feature extraction from lung and extracted features from left and right lung.  
My question is: is it possible to extract features from total lung?

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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:** [November 23, 2022, 8:17am UTC](https://discourse.slicer.org/t/covid-lung-radiomics-feature-extraction/26395/2 "2022-11-23T08:17:36Z")

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Yes, if you use Lung CT Segmenter and perform a lung segmentation, the module will create a segment “thoracic cavity” which - if you do not check “vessel segmentation” - will contain both the right and left lung.  
I´ll add a standard segment named “lungs” within the next few days.

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**Author:** ![Nima\_Yousefi](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/nima_yousefi/32/66845_2.png) [@Nima\_Yousefi](https://discourse.slicer.org/u/Nima_Yousefi)\
**Post date:** [November 23, 2022, 3:32pm UTC](https://discourse.slicer.org/t/covid-lung-radiomics-feature-extraction/26395/3 "2022-11-23T15:32:32Z")

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I have another question if you can help me @rbumm  
I checked “airway segmentation” then After radiomics features extracted, both image nrrd file and its labelmap(mask) nrrd file add to directory path and then “remove” from it.

Is it intended?

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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:** [November 23, 2022, 8:16pm UTC](https://discourse.slicer.org/t/covid-lung-radiomics-feature-extraction/26395/4 "2022-11-23T20:16:16Z")

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Do you mean the files that are displayed here?

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/9/0/90a509b4eee4b405033d589cc91a04d63185bc53.png)

They seem to be temporary files.

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**Author:** ![Nima\_Yousefi](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/nima_yousefi/32/66845_2.png) [@Nima\_Yousefi](https://discourse.slicer.org/u/Nima_Yousefi)\
**Post date:** [November 23, 2022, 8:46pm UTC](https://discourse.slicer.org/t/covid-lung-radiomics-feature-extraction/26395/5 "2022-11-23T20:46:43Z")

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Yes exactly  
Actually I’m looking for a binary mask like this:

 ![Screenshot_20221123-112422_Firefox](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/9/7/97cb7bd3f12c05eb221d64077942663e9c1bea43.jpeg)

How can I create something like this in slicer?

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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:** [November 24, 2022, 9:04am UTC](https://discourse.slicer.org/t/covid-lung-radiomics-feature-extraction/26395/6 "2022-11-24T09:04:07Z")

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> [@Nima\_Yousefi](#):
>
> How can I create something like this in slicer?

You could run Lung CT Segmenter, then go to “Data”, right-click “Lung Segmentation” and “Export visible segments to binary labelmap”:

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/b/4/b4ef19b4f317e567d4a1af3fdf455c15d6cfeb23.png)

Of course, many other options exist in 3D Slicer’s “Segment Editor” to create binary masks.

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**Author:** ![Nima\_Yousefi](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/nima_yousefi/32/66845_2.png) [@Nima\_Yousefi](https://discourse.slicer.org/u/Nima_Yousefi)\
**Post date:** [December 1, 2022, 2:57pm UTC](https://discourse.slicer.org/t/covid-lung-radiomics-feature-extraction/26395/7 "2022-12-01T14:57:19Z")

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Hello Dr bumm.  
I have one question  
Did “lungs” segmenter added to lung segmenter option in the lastest slicer update?

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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:** [December 1, 2022, 3:31pm UTC](https://discourse.slicer.org/t/covid-lung-radiomics-feature-extraction/26395/8 "2022-12-01T15:31:13Z")

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Yes, “lungs” now get automatically created upon your request (Slicer 5.2.1), but you would need to checkbox them in “Data” as “visible”.

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/1/a/1a1cef60dd477760d866a027c9caec10ad5fbc02.jpeg)

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<div class="post-metadata">

**Author:** ![Nima\_Yousefi](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/nima_yousefi/32/66845_2.png) [@Nima\_Yousefi](https://discourse.slicer.org/u/Nima_Yousefi)\
**Post date:** [December 6, 2022, 7:10am UTC](https://discourse.slicer.org/t/covid-lung-radiomics-feature-extraction/26395/9 "2022-12-06T07:10:27Z")

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Hello Dr bumm.  
is it possible to show radiomics features like glcm on the ct images in the slicer?  
Example:

 ![Screenshot_20221206-103027_Drive](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/a/6/a6f619fea8515917934380edf9ac40dde581b0e9.jpeg)

Best regard.

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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:** [December 6, 2022, 9:52am UTC](https://discourse.slicer.org/t/covid-lung-radiomics-feature-extraction/26395/10 "2022-12-06T09:52:02Z")

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Hello @Nima_Yousefi ,

This is an interesting question, I do not have a direct solution and am not aware of a pyradiomics voxel-mapping 3D Slicer function.  
You may need to run voxel-based radiomics from the command line to obtain the results you are aiming for.

Could maybe @JoostJM or other specialists comment, thank you.

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<div class="post-metadata">

**Author:** ![Nima\_Yousefi](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/nima_yousefi/32/66845_2.png) [@Nima\_Yousefi](https://discourse.slicer.org/u/Nima_Yousefi)\
**Post date:** [January 3, 2023, 7:14pm UTC](https://discourse.slicer.org/t/covid-lung-radiomics-feature-extraction/26395/11 "2023-01-03T19:14:21Z")

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Greeting Dr bumm  
about Shape, Texture, First Orderfeatures (like mean, autocorrelation , flatness , …)

what is their unit of measurements?

Thanks.