Can anyone help me with vesselness filtering? my issue is that when I preview one fiducial point for arteries it looks okay but when I click on apply button it selects some part of skull as well with arteries. I am trying to extract arteries from CT Angiography. Any suggestions? I am not sure what I am doing wrong.
Vesselness filtering enhances visibility and contrast of vessels but usually does not perfectly extracts vessels from the entire image.
You may use vesselness image as master volume in Segment Editor to touch up results. For example, you can use Thresholding effect to do an initial extraction and clean it up by Scissors and Islands effects.
I have gone through all these tutorials already. But still I am unable to segment the arteries. Whenever I extract them from DICOM using thresholding and islands effect it comes with some part of skull as well. Is there any other way of extracting arteries other than thresholding?
Thank you in advance.
Thank you for the link Andras but it doesn’t solve my problem completely. I am attaching some pictures here. Actually grow from seeds effect is not able to extract all arteries. It is extracting only the once that I have painted and it is very difficult to paint each and everything. It was successful with Aorta because it was a single structure. Could you suggest something more?
You can start with simple thresholding, choosing threshold value so low that all vessels that you are interested are included. Then use that for masking and use Grow from seeds. This should allow very clear separation of bone from vessels.
However, if image is noisy and/or low-resolution, contrast filling is uneven, etc. then it may be hard to choose a threshold value that includes small vessels and you may need to do more manual work, e.g., with Paint effect or Draw tubes effect, with thresholding (Maskin settings / editable intensity range).
Do you have a baseline image without contrast? If yes, then you can subtract the background (with automatic motion compensation), which may help in segmenting smaller vessels and automatically remove bone.
Slicer does not have a dedicated tool for vessel extraction, even with contrast enhancement. VMTK does not help any better, at least in my experience.
You will find such tools with dedicated software made by CT OEMs. That’s what I see with radiologists in my health institution. They do every vessel segmentation nearly automatically, refining with mouse clicks on the vessels.
Slicer aims to be a more generic tool. The developer team does not have enough financial resources to target specific tasks by medical discipline in my view. I think you should accept that your aim cannot be reached.
For your specific problem, the image below shows the best I could get using Level Tracing/Flood Filling/Grow from seeds. As you can see, the arterial isolation extent is quite limited. The skull base is always merged with the internal carotid arteries in close contact to the bone. If the latter is segmented at the same time, it could have been isolated from the arteries at the skull base. But this implies a lot of painting before the final segmentation. This is not feasible in practice.
In general, contrast enhanced arteries are quite readily segmented when there is no intimate contact with bones and when they are of surgical diameters (fortunately!). Otherwise, distal arteries isolation remains a challenge.
For some reason, in recent years there have not been significant (funded) interest for developing/maintaining open-source vessel analysis tools. Maybe this is, as you say, because commercial tools already fulfill all the clinical and research needs. It is also possible that there are still unmet needs but there have not been research groups who could allocate grant funding for this.
The only “manual” steps needed were choosing a few parameter values, so the whole workflow could be easily made fully automated - requiring only a single click and some optional parameter adjustments from the user.