Creation of centerlines in 1D simulation

[Andrea Scaburri]

Hi I am a beginner user in SimVascular,
I am working to a project which consists in the creation of a simplified 3D model of the vessel network in the lower limb and then I have to perform a 1D simulation thanks to SimVascular software.

The final 3D model created represents both arterial and venous system linked together, as it is possible to see in the attached images. I have no problem when I import the model in SimVascular and when I extract the surface and with the identification of the caps. Nevertheless when I am going to create the centerline, the software returns only the shortest path that connects the inlet and outlet areas. Is there the possibility to create the centerline in all the pipes of the model?
I attached two screenshots from Paraview hpoing they could help to understand my issue.
Thanks

[Martin Pfaller]

Hi Andrea,

That's an interesting vessel network you have!

The problem might be that not all outlets are identified in SimVascular. The centerline will connect the inlet to all the outlets. So you have to create caps for the other outlets as well.

Let me know if you run into problems doing that. It that case, it would be helpful if you can upload your geometry for us.

Martin

[David Parker]

Hi Andrea,

I had a look at your model.

There are only two inlet/outlet caps, the downstream vessels are not capped but circle back to the caps. I don't think the centerline extract algorithm will work correctly for this type of model.

Martin, do you think the 1D solver would work for this model if centerlines could be created for it?

Cheers,
Dave

[Andrea Scaburri]

Hi Martin and David, thanks for your replays.
In order to proceed with my project I have truncated the model attaced in the original topic to represent the arterial network. In this case I can correctly create the centrelines, after I have imported the model and I have created the 1D simulation job. Anyway after following the steps show in your tutorial dedicated to 1D simulation, the simulation ends with the following error: "Simulation job X has failed with non-zero exit code-1".
I have not found on SimVascular documentation dedicated to imported models and I am wondering if the software is able to create centrelines from the model, the simulation does not work due to other causes not releated to model structure?
These are the steps that I follow for the simulation:
Create a project > In SV data manager I go to model and import the solid model > I confirm the extraction of the surfaces > I create caps with the "Fill holes w. IDs" option > I specify the type of surfaces (walls and caps) > I create a 1D simulation job > In 1D simulation window I select the Inlet cap and calculate the centrelines > then I complete Inlet and Outlet BCs and set Solver parameters (N of steps 1000, Time step size 0.001).
Then I click on "Create files for simulation" and it ends successfully with warnings, but when I click on run simulation it ends with "Simulation job X has failed with non-zero exit code-1".

I apologize for the length of my question, but I hope I was as clear as possible and I can help other users with my case.
Thanks in advice for your answers.

[Martin Pfaller]

Hi Andrea,

I'm happy that you're now getting the centerlines! One problem in your model might be that the centerline extraction and the 1D solver can't handle loops right now, but I don't think that's causing the error right now.

Can you upload your 1D input file? You find it in your project folder under Simulation1D.

Thanks!

Martin

[Andrea Scaburri]

Hi Martin,
I have attached here the entire folder of my project which contains all the information about the 1D simulation.
To upload the folder here I have removed the .vtp files releated to centerlines and model surfaces, let me know if you need also them.

Cheers,
Andrea

[Martin Pfaller]

Hi Andrea,

I'm sorry for taking so long to get back to you. I ran the simulation files and for me they complete without error. I uploaded them here:

https://drive.google.com/file/d/1OYepx- ... sp=sharing

Are you using the current version of SimVascular?

Martin

[Andrea Scaburri]

Hi Martin,

Thank you again for your time and your willingness, when I was runring the simulation I used "SimVascular 2020.04.06 (MITK 2018.4.2 VTK 8.1.1 ITK 4.13.2 Qt 5.11.3)", this was the last version avaiable when I have started my project, but now I see there is a new version but there is not an installer for Windows.

I have downloaded your simulation results successfully, but there is not the converted results folder, how can I convert the results you send to me?

Andrea

[Martin Pfaller]

You can convert the files in the GUI. Create a new 1D simulation, go to Convert Results, and enter the folder where the results are saved.

If you're using Linux or Mac OS, you can also download the svOneDSolver executable: https://simtk.org/projects/simvascular

[Charlie Bright]

Hi Dave and Martin,

Sorry to dig up an old thread, but I am also having an issues with loops in a centreline calculation.

My geometry is a coronary artery bypass graft so I can't truncate the model any further to simplify it.
When generating centrelines, the centreline now follows the path of the bypass to the coronary outlet and ignores the path of the native vessel.

Is there a way to force the centreline tool to have many inputs to one outlet?
Or do you know of a way to generate this kind of behaviour with VMTK and import that .vtp into SV for a 1D simulation?

Thanks,
Charlie