TotalSegmentator heartchambers high res not working

Ione_Ianniruberto · July 23, 2024, 4:33pm

Hi,
I have CT images and I would like to segment all the heart chambers using the heartchambers highres tool. However it works fine for some images while for others there are two possible outomes: it dosen’t recognize the left vetricle or the nii.gz file is genereted but is empty. How can I solve this problem? Is this releted to the image quality?
Thanks
Ione

lassoan · July 23, 2024, 4:33pm

Which Slicer extension are you using for this?

jamesobutler · July 23, 2024, 4:56pm

If using TotalSegmentator, I would suggest following up on this existing issue:

github.com/wasserth/TotalSegmentator

Poor cardiac segmentations, including highres

opened 08:52PM - 15 Jul 24 UTC

yakovdan

Hello, I'm using the latest TotalSegmentator to segment the heart in CT scans.… Visually inspecting the output I can see that the output is very roughly correct but large parts of the heart remain unlabeled. I suspect there's an issue with my preprocessing. My CT scans are composed of 512x512 slices with a pixel spacing of about 0.7mm and a slice thickness of 1.25mm. Axially, the scans are variable but include the chest and upper abdomen. Since TotalSegmentator expects 1.5mm slices, I've accounted for that by resampling. I've examined small dataset, a subset of TotalSegmentator's train dataset, and noticed that the slices are 255x255. I've also noticed that the orientation in the training dataset for Total Segmentator is such that the positive axial direction is from feet to head. I couldn't find any information on pixel spacing and any information at all regarding the heart_highres dataset, neither on github nor in the paper. Can you please specify in detail the input format parameters that TotalSegmentator expects, both for the "total" task and for "heart_highres"? I mean input dimensions in all axes, pixel spacings, slices thickness, orientations, etc. Thank you

lassoan · July 23, 2024, 5:53pm

@jamesobutler Thank you for the additional information.

@Ione_Ianniruberto I would recommend to check open issues in TotalSegmentator’s issue tracker. If others have already described similar behavior then add your comments there. If all other existing open issues are unrelated then you can create a new issue. Please post the link to the existing or newly created issue here (so that people who have similar questions can follow the discussion over there).

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TotalSegmentator heartchambers high res not working

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