Extract coronary

Hi all, I have a DICOM file of the whole human heart and chest. I need to: 1- extract part of the geometry, say the aortic root, from the whole geometry; 2- convert it to an STL format file. Anyone can please suggest (free) software (Windows and Mac) for the foregoing purposes? I am searching the internet I could find a variety of them though I am willing to hear your generous suggestions as well. Thank you!


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You should be able to do this in segmentation software such as ITK-SNAP or 3D Slicer.

I prefer to convert DICOMs to Nifti format first (I use an in-house MATLAB script for this but there are free converters available) so that they don’t eat all the space on my hard drive but it isn’t a necessity.

Load the image, you’ll be able to segment ( the most basic form of this is just drawing around the region yourself but there are automated ways to do it too) the image to create a surface mask, then in the export options should be able to export this mask as an STL. I know 3D slicer lets you export STL, you could even segment in ITK and then export as STL in Slicer.

Hope this helps,


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