# Inquiry Regarding TotalSegmentator V2 Compatibility with Rabbit Micro-CT Images for Lung Segmentation

**URL:** <https://discourse.slicer.org/t/inquiry-regarding-totalsegmentator-v2-compatibility-with-rabbit-micro-ct-images-for-lung-segmentation/32489>\
**Category:** Support\
**Tags:** segmentation, totalsegmentator\
**Created:** [October 30, 2023, 6:18pm UTC](https://discourse.slicer.org/t/inquiry-regarding-totalsegmentator-v2-compatibility-with-rabbit-micro-ct-images-for-lung-segmentation/32489 "2023-10-30T18:18:16Z")\
**Posts on this page:** 16\
**Page:** 1

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**Author:** ![cong\_lu](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/cong_lu/32/68041_2.png) [@cong\_lu](https://discourse.slicer.org/u/cong_lu)\
**Post date:** [October 30, 2023, 6:18pm UTC](https://discourse.slicer.org/t/inquiry-regarding-totalsegmentator-v2-compatibility-with-rabbit-micro-ct-images-for-lung-segmentation/32489/1 "2023-10-30T18:18:16Z")

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Dear TotalSegmentator Team,

Thank you for releasing the updated TotalSegmentator V2 software. I am a Master’s student in medical science, currently focused on the quantitative analysis of micro-CT images in a rabbit model.

I’m wondering if TotalSegmentator V2 is compatible with rabbit micro-CT images, specifically for lung segmentation?

Thank you for your time and assistance.

Best regards

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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 30, 2023, 7:58pm UTC](https://discourse.slicer.org/t/inquiry-regarding-totalsegmentator-v2-compatibility-with-rabbit-micro-ct-images-for-lung-segmentation/32489/2 "2023-10-30T19:58:13Z")

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Not really - this is the output of Totalsegmentatoir in a rodent micro CT

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/d/f/df7ff11d137bae9972579ea50780e1cd4744449f.jpeg)

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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 30, 2023, 8:02pm UTC](https://discourse.slicer.org/t/inquiry-regarding-totalsegmentator-v2-compatibility-with-rabbit-micro-ct-images-for-lung-segmentation/32489/3 "2023-10-30T20:02:32Z")

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And this is the output after manual lung segmentation by defining seeds

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/0/9/09dd3310e65be82d4194c25aa96ada46d5c2a856.jpeg)

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**Author:** ![cong\_lu](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/cong_lu/32/68041_2.png) [@cong\_lu](https://discourse.slicer.org/u/cong_lu)\
**Post date:** [October 30, 2023, 8:31pm UTC](https://discourse.slicer.org/t/inquiry-regarding-totalsegmentator-v2-compatibility-with-rabbit-micro-ct-images-for-lung-segmentation/32489/4 "2023-10-30T20:31:33Z")

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Dear rbumm,  
Thank you for your prompt reply. I have also tried LungCTSegmenter for lung segmentation for in micro-CT images, but the results are not satisfactory.  
Could you possible have any recommendations or suggestions that might improve the quality of the lung segmentation using micro-CT images?  
Best

 ![Screenshot 2023-10-30 at 4.21.02 PM](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/e/1/e15c73b2b5a39c966b974f3f760eeb520e001732.jpeg)

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**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/3622_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [October 31, 2023, 1:24am UTC](https://discourse.slicer.org/t/inquiry-regarding-totalsegmentator-v2-compatibility-with-rabbit-micro-ct-images-for-lung-segmentation/32489/5 "2023-10-31T01:24:27Z")

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I would love to be wrong, but my understanding is without retraining or at the minimum finetuning them using your own segmented data, there is not much you can do with models trained on human clinical dataset.

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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 31, 2023, 8:48am UTC](https://discourse.slicer.org/t/inquiry-regarding-totalsegmentator-v2-compatibility-with-rabbit-micro-ct-images-for-lung-segmentation/32489/6 "2023-10-31T08:48:09Z")

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Maybe this link may help:

> [@LungCTAnalyzer extension for lung CT segmentation and analysis for COVID-19 assessment](https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006/44):
>
> 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: 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 …

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**Author:** ![cong\_lu](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/cong_lu/32/68041_2.png) [@cong\_lu](https://discourse.slicer.org/u/cong_lu)\
**Post date:** [November 1, 2023, 7:59pm UTC](https://discourse.slicer.org/t/inquiry-regarding-totalsegmentator-v2-compatibility-with-rabbit-micro-ct-images-for-lung-segmentation/32489/7 "2023-11-01T19:59:37Z")

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Thanks dear rbumm. LungCT Segmenter works for the micro-CT images after changing the parameter from 2 to 0.2. but the result is not satisfied.

 ![Screenshot 2023-10-31 at 10.04.13 AM](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/6/7/679d9e35290c49e1ab53c170abaab271123939a7.jpeg)

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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 1, 2023, 8:47pm UTC](https://discourse.slicer.org/t/inquiry-regarding-totalsegmentator-v2-compatibility-with-rabbit-micro-ct-images-for-lung-segmentation/32489/8 "2023-11-01T20:47:24Z")

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Is this by manual placement of the segmentation seeds or by AI segmentation? Can you make a CT sample available?

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<div class="post-metadata">

**Author:** ![cong\_lu](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/cong_lu/32/68041_2.png) [@cong\_lu](https://discourse.slicer.org/u/cong_lu)\
**Post date:** [November 1, 2023, 9:00pm UTC](https://discourse.slicer.org/t/inquiry-regarding-totalsegmentator-v2-compatibility-with-rabbit-micro-ct-images-for-lung-segmentation/32489/9 "2023-11-01T21:00:05Z")

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Bot the manual seeds and AI work well for the Chest CT sample. My previous try was segmented by AI. Here is the manual placement seeds. The result still not good. And there is no change after placing more seeds on missing area.

 ![Screenshot 2023-11-01 at 4.57.55 PM](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/5/9/59ae67967a38ba00db54a115734558c41b55f168.jpeg)

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**Author:** ![cong\_lu](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/cong_lu/32/68041_2.png) [@cong\_lu](https://discourse.slicer.org/u/cong_lu)\
**Post date:** [November 1, 2023, 9:13pm UTC](https://discourse.slicer.org/t/inquiry-regarding-totalsegmentator-v2-compatibility-with-rabbit-micro-ct-images-for-lung-segmentation/32489/10 "2023-11-01T21:13:23Z")

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Dear rbumm,  
After processing Lung CT Analyzer using the lung segmentation generated, I’ve got some color ball in the image. I don’t think the colour balls affect the statistics results.

 ![Screenshot 2023-11-01 at 5.08.19 PM](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/e/3/e36e6e54669ea737ae92bb73326cf3d35f2642f8.jpeg)

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**Author:** ![diazandr3s](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/diazandr3s/32/9973_2.png) [@diazandr3s](https://discourse.slicer.org/u/diazandr3s)\
**Post date:** [November 2, 2023, 11:57am UTC](https://discourse.slicer.org/t/inquiry-regarding-totalsegmentator-v2-compatibility-with-rabbit-micro-ct-images-for-lung-segmentation/32489/11 "2023-11-02T11:57:47Z")

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I agree with @muratmaga on this:

`without retraining or at the minimum finetuning them using your own segmented data, there is not much you can do with models trained on human clinical dataset.`

@cong_lu have you considered training an AI model for this task using [MONAI Label](https://github.com/Project-MONAI/MONAILabel/tree/main)?

Here I showed how to organize the dataset and train a model: [https://youtu.be/-HAryYAO5J4?si=uxJPxrDuTDUE-zHr&t=560](https://youtu.be/-HAryYAO5J4?si=uxJPxrDuTDUE-zHr&t=560)

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<div class="post-metadata">

**Author:** ![cong\_lu](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/cong_lu/32/68041_2.png) [@cong\_lu](https://discourse.slicer.org/u/cong_lu)\
**Post date:** [November 2, 2023, 6:53pm UTC](https://discourse.slicer.org/t/inquiry-regarding-totalsegmentator-v2-compatibility-with-rabbit-micro-ct-images-for-lung-segmentation/32489/12 "2023-11-02T18:53:29Z")

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thanks for your suggestion. I’d like to use MONAI Label to train an AI model. I don’t have much experience in programming. I cannot understand the command part in your video. And I got the ERROR from MONAI Label when I start the module. Could you kindly guide me to solve the issue?

Traceback (most recent call last):  
File “/Applications/Slicer.app/Contents/Extensions-31938/MONAILabel/lib/Slicer-5.4/qt-scripted-modules/MONAILabel.py”, line 1072, in fetchInfo  
info = self.logic.info()  
File “/Applications/Slicer.app/Contents/Extensions-31938/MONAILabel/lib/Slicer-5.4/qt-scripted-modules/MONAILabel.py”, line 2263, in info  
return self.\_client().info()  
File “/Applications/Slicer.app/Contents/Extensions-31938/MONAILabel/lib/Slicer-5.4/qt-scripted-modules/MONAILabel.py”, line 2239, in \_client  
if mc.auth\_enabled():  
File “/Applications/Slicer.app/Contents/Extensions-31938/MONAILabel/lib/Slicer-5.4/qt-scripted-modules/MONAILabelLib/client.py”, line 83, in auth\_enabled  
status, response, \_, \_ = MONAILabelUtils.http\_method(“GET”, self.\_server\_url, selector)  
File “/Applications/Slicer.app/Contents/Extensions-31938/MONAILabel/lib/Slicer-5.4/qt-scripted-modules/MONAILabelLib/client.py”, line 521, in http\_method  
conn.request(method, selector, body=body, headers=headers)  
File “/Applications/Slicer.app/Contents/lib/Python/lib/python3.9/http/client.py”, line 1285, in request  
self.\_send\_request(method, url, body, headers, encode\_chunked)  
File “/Applications/Slicer.app/Contents/lib/Python/lib/python3.9/http/client.py”, line 1331, in \_send\_request  
self.endheaders(body, encode\_chunked=encode\_chunked)  
File “/Applications/Slicer.app/Contents/lib/Python/lib/python3.9/http/client.py”, line 1280, in endheaders  
self.\_send\_output(message\_body, encode\_chunked=encode\_chunked)  
File “/Applications/Slicer.app/Contents/lib/Python/lib/python3.9/http/client.py”, line 1040, in \_send\_output  
self.send(msg)  
File “/Applications/Slicer.app/Contents/lib/Python/lib/python3.9/http/client.py”, line 980, in send  
self.connect()  
File “/Applications/Slicer.app/Contents/lib/Python/lib/python3.9/http/client.py”, line 946, in connect  
self.sock = self.\_create\_connection(  
File “/Applications/Slicer.app/Contents/lib/Python/lib/python3.9/socket.py”, line 844, in create\_connection  
raise err  
File “/Applications/Slicer.app/Contents/lib/Python/lib/python3.9/socket.py”, line 832, in create\_connection  
sock.connect(sa)  
ConnectionRefusedError: [Errno 61] Connection refused

 ![Screenshot 2023-11-02 at 2.52.20 PM](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/9/2/9257cf8bd8da02ee3896294329932adbb85bfc9a.jpeg)

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<div class="post-metadata">

**Author:** ![diazandr3s](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/diazandr3s/32/9973_2.png) [@diazandr3s](https://discourse.slicer.org/u/diazandr3s)\
**Post date:** [November 2, 2023, 11:24pm UTC](https://discourse.slicer.org/t/inquiry-regarding-totalsegmentator-v2-compatibility-with-rabbit-micro-ct-images-for-lung-segmentation/32489/13 "2023-11-02T23:24:07Z")

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Hi @cong_lu,

MONAI Label comprises two parts: a server that hosts the AI models and a viewer part that connects to the server (i.e. 3DSlicer).

The server part can be installed and started following these instructions: [GitHub - Project-MONAI/MONAILabel: MONAI Label is an intelligent open source image labeling and learning tool.](https://github.com/Project-MONAI/MONAILabel#step-1-installation)

Unfortunately, the server part is being tested on Linux and Windows operating systems, not Apple OSs

I hope this helps,

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<div class="post-metadata">

**Author:** ![cong\_lu](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/cong_lu/32/68041_2.png) [@cong\_lu](https://discourse.slicer.org/u/cong_lu)\
**Post date:** [November 3, 2023, 3:14am UTC](https://discourse.slicer.org/t/inquiry-regarding-totalsegmentator-v2-compatibility-with-rabbit-micro-ct-images-for-lung-segmentation/32489/14 "2023-11-03T03:14:54Z")

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Thank you @diazandr3s for your reply. I’ll find a Windows PC and try to install the server. I’ve no experience with Python, which is a big challenge. I’ll keep you update.

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<div class="post-metadata">

**Author:** ![cong\_lu](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/cong_lu/32/68041_2.png) [@cong\_lu](https://discourse.slicer.org/u/cong_lu)\
**Post date:** [November 3, 2023, 4:04pm UTC](https://discourse.slicer.org/t/inquiry-regarding-totalsegmentator-v2-compatibility-with-rabbit-micro-ct-images-for-lung-segmentation/32489/15 "2023-11-03T16:04:42Z")

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Hello @diazandr3s ,  
monailabel-0.8.1 was successfully installed, but I was stuck in downloading sample apps. Could you help me check the message from cmd?

 ![Screenshot 2023-11-03 120107](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/a/3/a304bdaa073455c3f21aef608fb7b86db9f6b9b6.png)

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<div class="post-metadata">

**Author:** ![diazandr3s](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/diazandr3s/32/9973_2.png) [@diazandr3s](https://discourse.slicer.org/u/diazandr3s)\
**Post date:** [November 3, 2023, 6:19pm UTC](https://discourse.slicer.org/t/inquiry-regarding-totalsegmentator-v2-compatibility-with-rabbit-micro-ct-images-for-lung-segmentation/32489/16 "2023-11-03T18:19:18Z")

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Hi @cong_lu,

It seems you’ve installed monailabel but didn’t activate the Python env.  
Have you seen these instructions created by @rbumm?

> **[MONAI Label installation](https://projectweek.na-mic.org/PW37_2022_Virtual/Projects/MONAILabelLung/MONAILabel_Installation.html)**
>
> Website for NA-MIC Project Weeks

Please let us know