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 ima…

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

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

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 image…

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.

Maybe this link may help: [image] LungCTAnalyzer extension for lung CT segmentation and analysis for COVID-19 assessment Support 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…

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]

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

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]

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]

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 ? Here I showed how to …

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

Support

rbumm (Rudolf Bumm) October 31, 2023, 8:48am 6

Maybe this link may help:

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

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