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Sim4Life

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  • Installing Sim4Life and configuring licenses

    36 126
    36 Topics
    126 Posts
    D
    Thank you so much!
  • Working with CAD models

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    63 Topics
    225 Posts
    brynB
    preview (still working on the distance from e.g. F7 to F9) [image: 1757340222351-c2ee64b1-55df-41d6-9583-bd5832ceb962-image.png]
  • Working with models from the Virtual Population

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    273 Posts
    brynB
    The tutorials are, unfortunately, not automatically synchronized to the cloud version yet. We can make the new ones available soon, though. Sorry for the inconvenience. If you send me an email (lloyd @ zmt.swiss), I can forward the notebook to you. Cheers, Bryn
  • FDTD, Low-Frequency, Neuron, Mode-Matching, Flow, Acoustics, etc...

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    AntoninoMCA
    Dear @gotou, There is a fundamental misunderstanding here. The EM LF Electro Ohmic Quasi-Static solver, is frequency-independent. The complex part of the fundamental electro quasi-stati equation \nabla\cdot\tilde\epsilon\nabla\phi = 0 (see Sim4Life manual, "2.6.1.4 Choosing the Appropriate Low Frequency Solver") is not solved AT ALL, since it is assumed that you have chosen this solver after having evaluated that the condition $\sigma>>\omega \epsilon_r \epsilon_0$ is valid for all the tissues and materials in your simulation at the frequency of interest. How to quantify this condition is also explained in the manual. The frequency has not impact on your simulation at all when you choose this solver. If you are unsure whether the condition $$\sigma>>\omega \epsilon_r \epsilon_0$$ applies, then you should consider to use the QS solver (not Ohmic-Current dominated) solver that solves the full complex equation. This solver uses both the conductivity and the permittivity and is frequency dependent. Please read the manual before running any further simulation if you have not clear which limitations apply to each solver: this is very important to proceed further. However, as @bryn also pointed out, the problem is then to decide which dielectric properties should be used. I agree with his observation. If your application uses sufficiently small frequencies, i.e. up to several tents of kHz, we suggest that you use the Ohmic current dominated solver in combination with the LF-IT'IS tissue properties. If you want further help, you should mention the type of application (e.g. neurostimulation) and the frequencies of interest. We could suggest you further documentation and scientific literature.
  • Postprocessing results

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    118 Topics
    351 Posts
    S
    After running the simulation the results are saved on my computer as h5 file so I want to understand how the sensor readings are stored in the h5 file. I want to extract the current density value per voxel. Is it feasible if I have the result h5 file?
  • Scripting interface for Sim4Life

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    138 Topics
    432 Posts
    S
    I ran an EM simulation on a human phantom and need to extract the current density for each anatomical component (e.g., nerve, spinal cord) using the Sim4Life Python API. Can I programmatically obtain per-part current density values and save them to a CSV file? Can I compute the current through a specific nerve programmatically as well?
  • Running Sim4Life over a network

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    7 Posts
    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.
  • '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
  • 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
  • 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.
  • The effect of electromagnetic field on the temperature of human tissues

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  • S4L is unable to read and load my project

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    ali.oezenA
    THank you very much for the hints.
  • How to export images from Sim4Life Analysis Results

    image export png jpeg
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    M
    That works! If it's for a 2D plot, you can always right click and export the data to an excel or csv file and then work with that if you'd prefer
  • Optimal performance

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    SylvainS
    The full version has the same performance as the Light version: it can just deal with bigger problems. Note that the low-frequency solvers are not GPU-accelerated, so if you are using that the GPU is anyway not used. If you are using the FDTD solver instead, it is accelerated by the GPU but its performance might be severely affected by the frequency of your simulation (the lower the frequency, the more iteration the FDTD method has to do in order to reach convergence). If you are in a regime where the quasi-static approximations hold, I would strongly advise you to use the LF solvers.
  • Editing the excitation signal

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    SylvainS
    I think your signal was fine, but your settings for the Field Sensor need to be changed.
  • Invalid Bounding Box Error

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    SylvainS
    2kHz will probably not be feasible in most propagating media, because the wavelength will simply be too large compared to the grid resolution your geometry requires (leading to unreasonably large time steps). You might want to check for e.g. what your grid look like, especially the padding at the boundaries of your computational domain.
  • This topic is deleted!

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  • CEM43 / Arrhenius Thermal Damage

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  • how to model a bent wire with a fixed length?

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    S
    Thanks for the code. Actually I need to model some wires with the fixed length, with one part in the brain in different spots and the remaining out of the brain, It takes a long time to model each one and I'm looking for a way to make them in a shorter time. Thanks.
  • grid resolution of wire and insulation

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    S
    Thanks for your reply.