Coronary vessel segmentation on cardiac CT images

Short tutorial on using 3D Slicer for coronary vessel segmentation. Used segment editor tools: Surface Cut, Mask volume, Paint, Scissors.
- Download 3D Slicer: www.slicer.org
- Extensions: SegmentEditorExtraEffects
- Data set: MAGIX (phase 70%, downloaded from demo.kheops.on...)
For more information or help, please write to the Slicer forum: discourse.slic...

[@a4uxu]

After I use dual 3D, the model of Volume rendaring is displayed in both 3D view.

[@AndrasLasso]

If you create new views then showing existing content in those new view by default makes sense. That said, you have full control over what you want to display where. One easy option is to hide the node in all views by clicking the eye icon, and then drag-and-drop content into the views where you want to see it. Alternatively, to modify where a particular volume's 3D rendering is displayed you can check/uncheck views in Volume Rendering module -> Inputs -> View.

[@sunj3t]

Nice work. I would like to see you segment brain vessels from an Angio CT or a contrast MRI (harder). This is where "fun" begins.

[@AndrasLasso]

To get help with other vascular segmentation tasks, post your question on the Slicer forum - discourse.slicer.org - including a download link to a typical data set.

[@stefanbanev]

Why do not do a free hand cut directly on 3D, slice through 3D and scalp what you want, rotate and scalp more if needed... Why to do it so awkward through MPR

[@AndrasLasso]

We don't paint in the slice (MPR) views. Using Scissors would highlight every bright regions inside the heart and on the other side of the heart that you would need to later remove. If you use the Paint tool then it only segments bright regions around the paintstroke, so no cleanup is needed afterwards.

[@michakozowski8824]

I don't know why but during the step with volume masking the 2D images are updated correctly but the 3D image is not. All additional structures such as ribs stay in place, I cannot remove them even with scissors. What might be the problem?

[@AndrasLasso]

Most likely in the 3D view you show the volume using volume rendering or models exported from the segmentation. You can go to Data module and hide those. If you still have questions then post it to the Slicer forum at discourse.slicer.org

[@mikolajbuchwald]

A very nice segmentation!

[@asifraj321]

You did not show how to generate a 3D view at the beginning.

[@AndrasLasso]

It is shown in the first few seconds: to display 3D you can simply drag-and-drop the image (CardiacCirc70_cropped) from the subject hierarchy to the 3D view.

[@asifraj321]

@@AndrasLasso I am following exactly your steps but coronary artery not displayed on 3D view after using sphere brush on that. How can I get that?