How can I visualize torso and heart mesh in meshalyzer?

Question

Hello!

I ran a bidomain simulation in a torso+heart mesh. I am trying to see the activation on the heart and just have not been able to do it with meshalyzer.

I cannot load the torso mesh or get its surface (could that be that it is too heavy ?). I loaded only the heart mesh and the vm.igb result but I don't know if when I use meshtool, the order of nodes and elements is preserved because the results I see shows the start of stimulation all over the place and not in the nodes I selected. This also does not work all the time even though I ran the same simulation but in different meshes.

I have used meshalyzer before but only on heart simulations, never with the torso.

I have been trying to use the meshalyzer from here https://opencarp.org/q2a/1280/install-meshalyzer-on-windows11-64 and also the AppImage.

Is there something specific I should be doing to be able to see the torso and heart only results?

Thanks you,

Jimena

Answer 1

Hey,

normally, this should not be an issue. 

If you run bidomain simulations, your heart+torso mesh is split into an extracellular (everything belongs to this) and intracellular (only your heart tissue) mesh. As a result, the solutions of the bidomain equation, i.e. phi_e and vm are only available for those meshes & corresponding indexing. If you now try to visualize your results for vm.igb on your input mesh, it will not work and should give you an appropriate error message that the number of nodes in your mesh and solution don't match.

The most convenient way to get the correct meshes is to use the runtime parameters gridout_i=3 and gridout_e=3 during your simulation. 

I don't have an appropriate example at hand to test if there is a way to use meshalyzer after the simulation was done already.

If that is not the issue and your input mesh does not open at all, please give more details about potential errors etc. so we can take a look at it.

Best,

Tobias