Dear Team,
I managed to segment an aorta and a coronary tree with VMTK and Slicer. However for my case I would also like to extract calcifications present in the coronaries. I managed to threshold the calcifications, but from what I got from clinicians the calcifications are not completely surrounded by lumen. So I would need a way to make the calcifications stick to parts of the wall. Is there any way of achieving this? I attached a screenshot of my current segmentation.
Best regards
Elias
Hi,
This is an interesting project.
Cant´you just âhollowâ the vessel segmentation, then âaddâ the calcification segmentation via âlogical operatorsâ ?
Regards
rudolf
Hi Rudolf,
thanks for your answer. I tried this but since the hollow algorithm removes symmetrically it will shrink the lumen also at the side where thereâs no calcification present or?
Do you have a test dataset available?
Hi, sorry for the late response, I was on vacation.
under this link you will find the dataset Iâm currently working on.
best regards
Elias
Made the âCOMBINEDâ segment hollow with a thickness of 0.3 mm and enabled the âCALCâ segment.
Hi Rudolf,
yes Iâm also quite happy with the segmentation, but the cardiologists I showed this dataset to told me that the calcifications are too much floating in the coronaries, they need to be stuck closest to the lumen wall, thatâs why I started to redo some things and asked myself if I can get around without to much manual work.
First of all, I think you need to rework your calcification (CALC) segmentation a bit.
This slice
produces this segmentation:
which may just be a little overdone in size and smoothed too much.
From the literature, the thickness of the coronary artery wall is around 0.75 mm.
Use this as the thickness in the âHollowâ tool With the hollow tool settings of
thickness: 0.75 and
Use current segment as: medial surface
I get this result
with your segmentation which leaves the calcifications sticking or very close to the artery walls.
If you rework the CALC segmentation maybe you can switch to
Use current segment as: inside surface
which should actually be the case here.
⌠you may also try a combination of volume rendering as shown here:
and adding the calcifications as separate segmentations
Hi Elias,
May I ask how you segmented the coronary arteries and what threshold you are using to identify the calcifications? Thanks in advance!
I could segment the LAD with this tool (with calcifications outside the lumen). The key part is placing control points as close as possible to its center for such small arteries. Thatâs tedious still.
Used parameters :
27 control points
Intensity tolerance : 60
Neighbourhood size : 2.0
Tube diameter : 4 mm
The calcifications were segmented with usual tools of the âSegment editorâ:
Threshold
Masking
Paint : with sphere brush in 3D.
Centerline extraction failed, I suppose because of a very tight stenosis.
N.B : This tool is still experimental and not conventional inside. And itâs one tube at a time.
Regards.
@chir.set Can you share which tool you used (link doesnât work), is this tool available as a module in 3D Slicer?
Yep, I even forgot I ever had this repository.
Itâs Guided artery segmentation module in the SlicerVMTK extension. Many things have changed since this post. If you have segmented a coronary, you can segment the calcifications very quickly with Arterial calcification pre-processor module in the same extension. Other kinds of tinkering can be helpful to segment coronaries when they are not too diseased, itâs still tedious however. Since I donât work with these arteries, I did not spend too much time with this.
