ZMT zurich med tech

Hi, I strongly recommend you have a look at the tutorial 3.2.12 called Temporal Interference with Complex Head Model. It should be of significant help for setting up a TI simulation correctly. As for your specific questions: yes, that's correct. You can actually get the full Python script that generates a given simulation from the GUI by right-clicking on the simulation in the Explorer tree and selecting "To Python". Very useful :) That will most likely not work. Instead, you should apply fixed voltage Dirichlet conditions (e.g. +/- 1V) and re-normalize your results at post-processing (see screenshot below) For most fields that you can see in the analysis, you can use the Imp/Export menu in the ribbon and find a format in which to export (e.g. Matlab, VTK, or even plain text). [image: 1756718002390-0c790cba-feab-4bf1-a1c2-c6c1b959649c-image.png] [image: 1756718129268-fdbe02f0-7b3a-4d2e-a68d-989752dd05a7-image.png]

Hi @AntoninoMC, I really appreciate this answer as it helped clear some things up for me. I understand the current extractor much better than I did before and I've realized why I may have been running into some issues. The method of using the analysis as a source also seems to be preferable. I am using the EMLF Electro Quasi-Static model for modelling transcutaneous spinal cord stim, for which precise control of the current is of absolute importance. The multiplier method seems to be the way to go for feeding into the NEURON simulation, as it means I don't have to rerun my EMLF sim. One thing I'm wondering, when I select the analysis/cache as a source, I lose the ability to use the contact impedance model in the NEURON setup. If I use a contact impedance model producer to modulate the resulting EM field from the multiplier, I lose the ability to set pulse parameters, which then seems to prevent NEURON from running a simulation. Do you know if there's a way to use the analysis connection with a multiplier AND a contact impedance model simultaneously for driving a NEURON simulation?

The guided tours within the tutorials are indeed not working as intended. Thanks for pointing this out! Instead, I would recommend following the instructions in the text documentation of the tutorials: https://manual.sim4life.io/manual/Tutorials/index.html Let me know if you run into issues with a specific tutorial!

Hello, I have the same issue. Currently using Sim4Life 8.2.0.16876. I wonder if there is any new update on this. Many thanks, Ines

OK, I will share it. Thanks

Thank you so much!

If I understand correctly, you would like to have one simulation with a total current of 2.47mA and another one with 1.98mA. Sim4Life EQS solvers use Dirichlet boundary conditions for the electrodes (fixed voltage) as they solve for electric potential and electrode surfaces are assumed to be equipotential, hence the flux should be able to vary to ensure an equipotential surface. Moreover, when you check “Treat as port” for the LF solvers, you should be able to see in the log that they run 1 simulation per port, by setting this port to 1V and all the rest to 0V. With only 2 electrodes, and assuming you have one anode and one cathode, I would suggest the following: Assign Dirichlet boundary conditions to the electrodes (one setting per electrode, for instance 0.5V and -0.5V). Run the simulation Extract the total current of the simulation (select the "Overall Field" and use the "Current Extractor" from the ribbon). Normalize your fields of interest by the scaling factor: desired current/total current. Visualize the output of your normalized field. I hope this helps!

Hi @Seifeldin_E I assume you’re referring to the second row, where the field is shown on the surface of the spinal cord and peripheral nerves. Here’s the simplest way to achieve this: In the Field Sensor, select Current Density. Add a Masking Filter: Set selection to None (deselect everything). Type Nerve in the search filter and activate all nerve structures. Search for the spinal cord and activate it as well. Add a Surface Viewer — this will extract the surface at the masked regions. How it works: The masking filter replaces all unselected field values with NaN (not-a-number). The surface viewer detects NaN values and extracts the surface surrounding the masked voxels. Alternative method (less robust): Drag a TriangleMesh entity (e.g., Spinal_cord) to the Analysis tab. Select Current Density and the spinal cord mesh (now in Analysis, apply the Model to Grid filter). Add the Interpolation filter. Add a Surface Viewer Be aware: if the field changes abruptly near the surface, this method may interpolate the field on the "wrong" side of the surface. That’s why the masking approach is usually more reliable and easier to use.

your code is still not using the FieldInterpolationFilter to interpolate the T1w image onto the same grid as the E-field. Note, the FieldDataTextExporter takes the output of the interpolator as input

Hi there, I hope you can help, and that my questions fits within this thread. I have simulated an overall field and I would like to export it to matlab. At first I can live with the UI way i.e. by the import/export menu, but later I'd like to script it too. Now selecting e.g. the E-field and clicking the Imp/Export menu gives me no options but Import. Can anyone show the workflow? And/Or can anyone post a snippet of python code that does the export? Does exporting require a certain license?

@viniltc, the error looks like you do not have a simulation called "Simple ES" (the returned simulation is None). Please double-check the name, including white-spaces. You can also access by index (document.AllSimulations[0]).

it seems to happen (in Sim4Life 9.0.0) when you switch to the analysis tag after sending a solver job on the cloud. I guess it can be ignored and will be fixed in an upcoming update-fix release

Hi, Did you run your simulation using our SMALL server (16 CPU cores, 32 GB RAM) or the LARGE server (48 CPU cores, 96 GB RAM)? Also, could you let us know the total number of cells in your simulation? As a general suggestion for optimizing memory usage, you can start by running a simulation with a coarse grid to identify regions where the fields are negligible. Based on this, you can adjust the grid padding settings to exclude those body regions from the simulation domain, effectively "cropping" unnecessary areas and reducing the computational load.

I believe the Materials.db) is copied from C:\Program Files\Sim4LIfe XYZ\data\... when you first run Sim4Life.exe

Hi, sorry to bother you. Do you happen to know how to calculate the current absorbed by the electrodes and the impedance?

I ran the simulation again. This time it ran completely. Physical results the same but without any errors, i.e. the analysis section could indeed connect ports. So is there a random seed thing and a voxeling issue after all?

I used it to get information for high level workflows. It can also come with suggestions for code, obviously, but it often invents functions that don't exist and implementations for me has not been very AI-powered. But the theoretical discussions are quite good.

Here is the Web Manual section containing this information: 2.11.3.9 Neuro-stimulation with Imperfect Electrode-Skin Contact. Additionally, Yoon-Sun Arm Stimulation tutorial also includes this new feature. For more information or examples you can contact us at s4l-support@zmt.swiss. Thanks!

Please select the overall field and select the E field, then look under "Field Data Tools". Please "Go to the HTML manual" from "Help" and search for NaN filter. I would recommend using the latest version of Sim4Life v9.0. [image: 1753361215835-bc62f2dd-580a-4b6b-b11d-728454d14416-sim4life_xhh8cgbkwm.png]

I recommend checking out the “Multiple Electrode in Homogeneous Medium” tutorial in the LF section. It includes a Petri dish with solution in the modeling part, which is directly relevant. You're absolutely right about the importance of the Boolean Subtract order. To ensure it works correctly, try the following setup: (1) Outer Cylinder: Radius = 18 mm, Height = 11 mm, Base at Z = 0 mm (2) Inner Cylinder: Radius = 17 mm, Height = 10.7 mm, Base at Z = 1 mm (i.e., shifted +1 mm in Z) (3) Perform Boolean Subtract: Outer minus Inner This setup should produce the correct bowl shape.