Hello everyone.
I’m new here and this is my first post in community. If there is something you find wrong in this post, I can remove it if you contact me.
I am working on a project about the automatic segmentation of great arteries from CT images. I study engineering so that my anatomy background is not very good. I started to use a 3D slicer to segment aort and pulmonary arteries, but anatomy and selecting appropriate segmentation tools are hard for me. Can you suggest sources for these issues?
In addition, I want to ask another thing. I exported the segmentation of a dicom slice in NRRD format as a labelmap and read the NRRD file in Python. When I visualized this, I noticed that it was rotated compared to the segmentation I made in 3D slicer. Is that because of the fact that the Dicom and NRRD file keeps the axis records in different orders?
You can segment message vessels automatically using MONAIAuto3DSeg, TotalSegmentator, LungCTAnalyzer extension.
If a software displays an image incorrectly then you can report the error to its developers. If they don’t respond then you can try to fix the issue yourself or use a different software.
First of all, thank you for answering. I tried the 3 extensions you mentioned.
MonaIauto3dseg and Totalsegmentator returned very good segmentations than I expected.
The aorta has a understandable anatomy, but Pulmonary Arteries is a bit difficult. I couldn’t find a simplified source to define its anatomy. If you have a source about this, can you share it with me?
Before I see your answer, I tried to do it myself and I shared the result I made. With this, I plan to train a 3D U-Net model, and I will give the segmentation of 20 such volumes to the model by matching these slices with the corresponding labelmap, respectively. I really appreciate if you comment.
About Nrrd, I just asked because I was wondered, my goal was not to complain.
