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  • Installing Sim4Life and configuring licenses

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    G
    Did you do one of the following: • Define the FlexNet environment variable FLEXID_LIBRARY_PATH to point to the location of the dongle shared object, libhasp_linux_x86_64.so. • Define the system environment variable LD_LIBRARY_PATH to point to the location of the dongle shared object libhasp_linux_x86_64.so. ? Could you try to send us the output of lmhostid -flexid? that command should return the dongle id. You can also access the dongle firmware - if it is correctly installed - via the loopback address. On a browser, go to http://localhost:1947/ you should see the characteristics of the dongle. Let us know if it works.

  • Working with CAD models

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    V
    @brown Thank you for the suggestion. I can surface project object now.

  • Working with models from the Virtual Population

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    V
    That's helpful. Thank you for the detailed steps @bryn.

  • FDTD, Low-Frequency, Neuron, Mode-Matching, Flow, Acoustics, etc...

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    V
    Hi all, I'm running a low-frequency neurostimulation simulation on Sim4Life Web using the Electro Ohmic Quasi-Static solver on the Yoon-son complete anatomical model. Simulation settings: Frequency: 1000 Hz Electrodes: Two placed on the chest area Boundary Conditions: Flux boundary automatically applied to external bounding planes Dirichlet boundary applied to both electrodes (set as “Treated as Port”) The simulation took approx. 45 minutes to solve, but I encountered an error at the end. Here are the last lines of the log: 2025-05-30T11:23:35.790Z [INFO] [XCore.CLog] Iteration 4 and residual drop factor 5.33458e-06 2025-05-30T11:23:35.791Z [INFO] [XCore.CLog] JSON PROGRESS : [Info] {{{"descriptor":"Solving linear system: Real Part","permill_completed":430,"type":"0","version":"0"}}} 2025-05-30T11:24:04.150Z [INFO] [XCore.CLog] Iteration 5 and residual drop factor 8.98461e-07 2025-05-30T11:24:04.152Z [INFO] [XCore.CLog] JSON PROGRESS : [Info] {{{"descriptor":"Solving linear system: Real Part","permill_completed":500,"type":"0","version":"0"}}} 2025-05-30T11:24:32.557Z [INFO] [XCore.CLog] Iteration 6 and residual drop factor 4.14111e-07 2025-05-30T11:24:32.558Z [INFO] [XCore.CLog] JSON PROGRESS : [Info] {{{"descriptor":"Solving linear system: Real Part","permill_completed":530,"type":"0","version":"0"}}} 2025-05-30T11:25:00.816Z [INFO] [XCore.CLog] Iteration 7 and residual drop factor 4.9417e-08 2025-05-30T11:25:00.818Z [INFO] [XCore.CLog] JSON PROGRESS : [Info] {{{"descriptor":"Solving linear system: Real Part","permill_completed":600,"type":"0","version":"0"}}} 2025-05-30T11:25:29.127Z [INFO] [XCore.CLog] Iteration 8 and residual drop factor 1.48857e-08 2025-05-30T11:25:29.128Z [INFO] [XCore.CLog] JSON PROGRESS : [Info] {{{"descriptor":"Solving linear system: Real Part","permill_completed":650,"type":"0","version":"0"}}} 2025-05-30T11:25:57.655Z [INFO] [XCore.CLog] Iteration 9 and residual drop factor 2.25318e-09 2025-05-30T11:25:57.657Z [INFO] [XCore.CLog] JSON PROGRESS : [Info] {{{"descriptor":"Solving linear system: Real Part","permill_completed":720,"type":"0","version":"0"}}} 2025-05-30T11:26:25.941Z [INFO] [XCore.CLog] Iteration 10 and residual drop factor 2.95529e-10 2025-05-30T11:26:25.942Z [INFO] [XCore.CLog] JSON PROGRESS : [Info] {{{"descriptor":"Solving linear system: Real Part","permill_completed":790,"type":"0","version":"0"}}} 2025-05-30T11:26:54.268Z [INFO] [XCore.CLog] Iteration 11 and residual drop factor 6.34014e-11 2025-05-30T11:26:54.270Z [INFO] [XCore.CLog] JSON PROGRESS : [Info] {{{"descriptor":"Solving linear system: Real Part","permill_completed":840,"type":"0","version":"0"}}} 2025-05-30T11:27:22.560Z [INFO] [XCore.CLog] Iteration 12 and residual drop factor 1.48467e-11 2025-05-30T11:27:22.562Z [INFO] [XCore.CLog] JSON PROGRESS : [Info] {{{"descriptor":"Solving linear system: Real Part","permill_completed":900,"type":"0","version":"0"}}} 2025-05-30T11:27:50.924Z [INFO] [XCore.CLog] Iteration 13 and residual drop factor 1.8532e-12 2025-05-30T11:27:50.926Z [INFO] [XCore.CLog] JSON PROGRESS : [Info] {{{"descriptor":"Solving linear system: Real Part","permill_completed":970,"type":"0","version":"0"}}} 2025-05-30T11:28:19.032Z [INFO] [XCore.CLog] Iteration 14 and residual drop factor 3.03701e-13 2025-05-30T11:28:19.035Z [INFO] [XCore.CLog] JSON PROGRESS : [Info] {{{"descriptor":"Solving linear system: Real Part","permill_completed":1000,"type":"0","version":"0"}}} 2025-05-30T11:28:19.037Z [INFO] [XCore.CLog] Elapsed time for 'Solving linear system: Real Part' was 00:07:06 wall clock time. 2025-05-30T11:28:19.039Z [INFO] [XCore.CLog] Solved linear system: Current and peak CPU memory usage: 42.5 GB / 42.5 GB (current is 100.0 % of peak) 2025-05-30T11:28:19.041Z [INFO] [XCore.CLog] Solver returns: 'converged (relative tolerance)'. 2025-05-30T11:28:21.522Z [ERROR] [XCore.CLog] 2025-05-30T11:28:21.524Z [ERROR] [XCore.CLog] The solver process failed to exit correctly: eExitFail The solver fails to exit cleanly. During the run, I observed CPU memory usage jumping from about 40% to 100% at times. Could this indicate that memory limitations caused the eExitFail error? Has anyone seen a similar issue with large anatomical models? Any suggestions on how to debug or avoid this error? Thanks in advance

  • Postprocessing results

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    brynB
    You could probably export (XPostProcessor.VtkExporter or XPostProcessor.VtkXmlExporter, not sure it is in s4l_v1) it as a VTK file and modify your neural network DataLoader to support VTK files, e.g., via the meshio package or the much larger vtk package, or many others. Or you could write a little Python script to grab the field data and save it to npy. To access the field, you would get the output of the extractor or pipeline entity in the analysis, say a FloatFieldData object. It has a Field(self, index: int) -> np.ndarray method to get the field as a numpy array, which you could save using e.g., np.save("filename.npy", fd.Field(0))

  • Scripting interface for Sim4Life

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    brynB
    do you have a screenshot of the model entities (showing the explorer and 3d view)? it would help a lot to clarify your description. If you really have a tetrahedral mesh, does this mean you have an unstructured simulation (or is it rectilinear)? Do you get an error message (can you copy it here)? We can check the different model entity types, to see if something doesn't work there.

  • Running Sim4Life over a network

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    ofliO
    Hi, Please allow me to share here the response we sent you via the Sim4Life support email so that other users can benefit from your questions. The default machine provides 500GB of storage, and you are running out of space for this project. If your results require more than 500GB, consider upgrading to a higher-tier machine with greater storage capacity. Alternatively, you could reduce the size of your simulation project by splitting it into multiple smaller simulations. This would allow you to continue using the default tier. Additionally, you might optimize your sensor settings, such as by creating smaller sensors and recording data for specific volumes of interest, rather than using an Overall Field sensor.
  • K

    This topic is deleted!

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  • R

    Volt and sensitivity of transducer sim4lite

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    M
    Assuming a linear relation between voltage and pressure amplitude, you should be able to map the input voltage to the input pressure (I think its 1 MPa by default), and then use this as a scaling factor, but it's unclear to me what you mean with voltage at the focused area. What exactly do you mean by transducer sensitivity? You could run additional simulations where you shift the transducer or slightly change some parameters to get a sense of the sensitivity.
  • A

    How to Script the Import a Segmented NIfTI Volume as a Solid in Sim4Life?

    image model python
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    brynB
    Here is a simple implementation to write an iSEG tissue list file, given a dictionary mapping the label index to a name: https://github.com/dyollb/s4l-scripts/blob/df8e2241f87ca91d71138e9d2b3d4336dadb82dc/src/anisotropic_conductivity/load_labels.py#L44
  • vegogardenV

    This topic is deleted!

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  • J

    Cannot open .smash project file

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    J
    Thank you so much you are a godsend 🙏 You saved me a couple days worth of work!
  • L

    Heat generation rate and Heat transfer rate in a MQS/Thermal simulation

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    H
    In terms of the material settings in the thermal simulation: The heat transfer rate defines whether heat removal by perfusion should be considered. In the absence of this term, heat is only removed by thermal conduction (diffusion) and boundary conditions. The options provided for heat transfer rate affect whether perfusion is constant or affected by local thermoregulation (temperature (T) dependent perfusion, e.g., to account for vasodilation). As for the heat transfer rate, the heat generation rate term can be constant or affected by local thermoregulation (T dependent, reflecting increased metabolic activity with increasing temperature). It is also possible to introduce time-dependent heat generation, e.g., to model a heating battery. Baseline perfusion values (incl. variability information) are available in the IT'IS database and can be automatically assigned from sim4life: (http://www.itis.ethz.ch/virtual-population/tissue-properties/database/database-summary/). If non-constant perfusion should be applied or not depends on the tissue and temperature increase magnitude (e.g., muscle above 39 starts to have a strong perfusion increase). The conservativeness of a perfusion model choice is application-dependent. To simulate the heating effect of tissues over time, blood perfusion and heat generation rate (metabolic heat generation) of the tissue would also need to be considered. The perfusion is covered in the option "Heat Transfer Rate". All options that you can enter here are related to heat-transfer based removal of energy from the system. Perfusion can be adjusted by changing the type of hear transfer (None, Constant, Linear (T), Piecewise Linear (T). The constant term assumes constant perfusion, independent of tissue temperature. It is the default assigned when using the IT'IS tissue database in Sim4Life. Linear (T) or Piecewise Linear (T) assume temperature dependent perfusion. You can add your your transition temperatures using the little "+" icon. Please note that the linear coefficients represent the slope of the linear perfusion. Each transition temperature indicates the change of the perfusion rate.
  • Paria M.P

    Grid Convergence

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    B
    To perform such a study, define your region or quantity of interest, then parametrize it. After a quantity has been parametrized, you can run multiple simulations using the built in Sweeper feature or using the Sim4Life Python API. There is an example in the Sim4Life manual titled 'Parametrized Patch Antenna' that shows how to use the Sweeper feature. If using the Python API, the easiest way would be to create a baseline simulation by hand, then right-click on the simulation name and select To Python. Then you would find the quantity of interest in the auto-generated script and assign it to a variable instead of the hardcoded value. Using a simple loop in Python, you can create multiple simulation that have identical setup except for parameters of interest. In your example, multiple simulations would be run with identical setup except for the grid resolution within a region of interest (e.g., a wire block surrounding a region of interest is placed in a manual grid settings folder, then Maximum Step is changed from 0.3 to 1.0 mm). Then in Analysis you extract a quantity of interest and compare how this value changes as a function of grid resolution. If the change in the value is small as you increase resolution, you can proceed in future simulations with a coarser resolution to save on run time. The exact convergence of the value needed depends on your application.
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    This topic is deleted!

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  • D

    My S4L file isn't opening after it crashed

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    D
    @bryn Thank you Bryn. Managed to find a version that wasn't corrupted! Hope you have a nice day :)
  • L

    3D Surface model to Voxel and export

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    brynB
    Are you using Sim4Life lite (web version)? I recorded my screen while I voxeled Duke V2.0 and exported the voxels. There seems to be a glitch in the Reload button when I try to see the data that was saved in the Study: as a workaround the Reload button in the DATA tab works. I voxeled at 15mm, so the skin is not completely closed, but if you choose something like 5-10mm it should be enough to resolve thin layers (like the skin): BTW. if you are using a desktop version of Sim4Life, the workflow is similar, except that the software uses native Windows file dialogs to save/load files. https://youtu.be/uAQgQQpG3Bg
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  • glasshousemediaG

    This topic is deleted!

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  • A

    Simulate a concave multi-element ultrasound array

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    M
    Assuming 'sim' is the acoustic simulation you're interested in and that 'elements' is a list of the elements (gotten from entities = model.AllEntities()) and that 'amp' and 'phase' are numpy arrays with the amplitude, phase values you're interested in assigning: # Print current simulation name print(sim.Name) # Remove all sources before adding them to_del = [] for s in sim.AllSettings: if isinstance(s,acoustic.SourceSettings): to_del.append(s) for d in to_del: sim.Remove(d) # Add sources with correct element and parameters for source_idx in np.arange(len(elements)): source_settings = acoustic.SourceSettings() source_settings.Amplitude = amp[source_idx] source_settings.Phase = phases[source_idx] sim.Add(source_settings, rings[source_idx]) print(rings[source_idx].Name, amp[source_idx], phases[source_idx]) Sorry I'm not providing a full example. Easiest way to do that would be to manually create the whole simulation without the sources (just make all sources as materials), then right click on simulation and select 'To Python...' and then add the lines above to your code You could do something like this to get the elements as a list: src_ents = [] entities = model.AllEntities() for e in entities: if 'Element' in e.Name: src_ents.append(e) Careful, I have no idea how the elements will be sorted in that case but you could use a fixed size numerical suffix and then sort them.
  • B

    File .Smash error

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    M
    Hallo, There should be, in the same folder where the smash project is, a file named as the smash file, but starting with a ".", like ".Name_of_the_File.smash.xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx". Try to drag that file directly into Sim4Life and save it with a different name. From there you should be able to go on with the models/simulations/analysis settings already saved.
  • L

    Cannot read document verion

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    L
    I have two versions installed (6.2.2 and 7.00) and I tried opening the file with both. I have now deleted the smash file that wasn't working and started over, but if it happens again, I will try the import option- thanks!
  • V

    Bone identification using RF signals

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  • S

    The file I created with Sim4Life light cannot be opened.

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    brynB
    If you don't have a full version, i think (untested) you can still recover the model by importing the smash file in the modeling tab.
  • P

    'Point Sensor Tool' is not available

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    M
    Sorry, don't have S4L with neuron available at the moment, but I looked at the tutorial and it seems to have changed. When you create the sensor settings can you try to drag and drop the axon to the sensor setting and then chose the section name? (That was the old way of doing it) Still, you should be able to run the simulation without a point sensor.. Sorry can't help more
  • L

    Everytime I'm doing a too complex simulation the file is lost

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    L
    I am using Sim4Life 6.2.1.4972. It happened once when I've had put a high "maximum number of samples" in the time domain (200 I think) with the acoustic head tutorial that I changed a bit, by putting 2 transducers instead of 1. Another time it was weird because it happened with a SEFT targeting a square of skin, which was rather simple but it did crash again. My simulation was probably wrong in a way, but it didn't throw and error and just stopped. But now that I am applying @gbgbha advices, it is fine :) and thanks for the tip ! I'll try for the file that I lost
  • R

    Why does TRP exceed input power(Antenna)?

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    SylvainS
    The TRP is computed in a different way than the input power. Both ways are mathematically correct and would both be "exact" if there were no numerical errors. In any FDTD simulation, however, there are spatial (finite grid) or temporal (finite time step) discretization error. What you are seeing in this half-wave dipole example, is that those discretization errors are larger than the precision you would require to distinguish TRP from input power (because the radiation efficiency is very high in this case, there is almost no difference between TRP and input power). To solve this "problem", either you accept that the simulation results are accurate enough for your needs (the warning is a simple consistency check) or you increase the precision of the simulation. You can do so by increasing the grid resolution, the overall convergence level and the resolution of the far-field sensor. This will be computationally expensive, though. To help you understand, you could try to add some lossy media in your (coarse) simulation (e.g. place the dipole next to a phantom or any other dielectric). The simulation will not be more precise, but the numerical errors will be less "obvious" because they will be dwarfed by the losses occurring in the dielectric. The TRP will be lower than the input power and the warning will not be triggered. I hope this helps.