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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

    63 225
    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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    59 Topics
    280 Posts
    T
    @halder I hope this message finds you well. I am currently conducting a temporal interference (TI) simulation using the LF Electro Ohmic Quasi-Static solver in Sim4Life, and I have encountered an issue regarding the electric field distribution at the electrode–skin interface. Here are the specific settings I used: There are four electrodes in total. For the first pair of stimulating electrodes, I assigned PEC material type to the other two electrodes (which are not used for stimulation). The stimulating electrodes were not assigned a material type; instead, I only applied Dirichlet boundary conditions to them. In the voxel settings, the four electrodes were set with priority = 1, and the Duke model with priority = 0. For the second pair of electrodes, I applied the same procedure accordingly. However, during post-processing, I noticed that the region where the electrodes overlap with the skin shows no electric field distribution, which seems physically unreasonable. Could you please advise if there might be an issue with my setup or if there are additional steps required to properly model the electrode–skin contact in TI simulations? Thank you very much for your time and support. I truly appreciate your help.

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

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    258 Topics
    775 Posts
    G
    Dear Geremia, Here is the procedure I use for S4L: Prerequisites: The Yale Neuron compiler 8.2.6 for Windows https://github.com/neuronsimulator/nrn/releases/tag/8.2.6 You can use newer versions, but this one works best with S4L. Create a directory for a particular neuron structure, at root level: hoc files, asc, etc. a subdirectory called 'mechanisms': all your mod files. From a console, run the Yale Compiler on your 'mechanisms' directory: > nrnivmodl if it succeeds, it will create a nrnmech.dll file. move the nrnmech.dll file to root level (where your hoc files are) and clean the 'mechanisms' directory - all the .c and .o files. Compress into a zip file the main directory (that contains the hoc files, nrnmech.dll and 'mechanisms' dir). Change the extension to .hocz Now, in S4L use the import button to import your new neuron model, your newly created hocz file. Regards, Guillermo

  • Postprocessing results

    121 372
    121 Topics
    372 Posts
    2
    Thank you for your response. Additionally, I would appreciate it if you could tell me how to output the temperatures from the thermal simulation results to text files, spreadsheets, Excel, etc. Ideally, I would like to be able to extract the temperatures at specified coordinates or average values for each model (Lung, Spleen, etc.). If specifying the model is difficult, it would also be acceptable to obtain the post-simulation temperature at specified coordinates.

  • Scripting interface for Sim4Life

    139 435
    139 Topics
    435 Posts
    brynB
    Btw, this topic is quite similar https://forum.zmt.swiss/topic/735/the-shape-of-the-t1-image-and-the-shape-of-the-electric-field-are-different

  • Running Sim4Life over a network

    4 7
    4 Topics
    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.
  • 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.
  • D

    The effect of electromagnetic field on the temperature of human tissues

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  • A

    S4L is unable to read and load my project

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    ali.oezenA
    THank you very much for the hints.
  • E

    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
  • A

    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.
  • J

    Editing the excitation signal

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    889 Views
    SylvainS
    I think your signal was fine, but your settings for the Field Sensor need to be changed.
  • J

    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.
  • H

    This topic is deleted!

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  • S

    CEM43 / Arrhenius Thermal Damage

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  • S

    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.
  • S

    grid resolution of wire and insulation

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    S
    Thanks for your reply.