STL Extraction from CT scans

Hello all,

I am new to the forums and I am reaching out to ask a question regarding segmentation and 3D STL extractions from CT scans compared to MRIs. So far I am had no issues trying to extract the ventricular system (lateral and third) using MRI DICOM scans. However when I try to do the same with CT scans instead the quality is extremely bad and results in very poor 3D renders of the ventricular system. I am able to get great 3D renders of the skull using CT scans but extremely bad renders for the ventricles.

I wanted to ask if using CT scans for the ventricular system is just not possible and I am better off with MRIs or if perhaps I am using the wrong settings for CT scans. Currently for MRIs I use the segmentation tools with the right threshold to get my lateral and third ventricles and I am able to make perfect 3D models. When I apply the same technique with CTs it is extremely bad even with varied threshold settings.

Thank you all for the feedback!

Yes, CT provides less soft tissue contrast than MR. I would suggest trying SynthSeg on your CT. It’s not available directly in Slicer but you can run it outside and easily load the results.