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

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

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    AntoninoMCA
    @KK The titration procedure provides a scaling factor that must be applied to the stimulation source (incident E-field, input current, or voltage applied at electrode pairs) in order to initiate an action potential in a fiber or neuron. Here are some examples depending on the stimulation source: Source: Incident E-field (e.g., induced by TMS) Assume the incident electric field is 1 V/m, and the titration procedure yields a titration factor, tf. The threshold E-field is therefore tf [V/m]. If this 1 V/m field results from a coil current rate of change dI/dt = A [A/s], then the threshold dI/dt required is A × tf [A/s]. Source: Applied voltage Let the applied voltage across an electrode pair be V = V₀. This value is also used as the Dirichlet boundary condition in low-frequency (LF) simulations. If the titration factor is tf, the threshold voltage becomes V₀ × tf [V]. Source: Applied current Let the applied current to an electrode pair be I = I₀, typically derived from LF simulations via a current flux integrator. With a titration factor tf, the threshold current is I₀ × tf [A]. The titration factor tf is a dimensionless number that gains physical meaning when applied to the relevant stimulation quantity (electric field, voltage, or current). @LJ was suggesting the correct course of action. I hope this clarification is helpful!
  • Simulations fail when multiple simulations are submitted

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    By default, Sim4Life tries to use all available resources to start as many simulations as you submit or have cores or GPUs available. The first simulation usually starts fine, and the rest fail due to insufficient licenses. You have the option to limit the number of simultaneous simulations in the ARES tool. Please change the Resource Management Option from Concurrent Jobs to One Job at a time as in the attached screenshot. [image: 1569997460703-ares3.jpg]
  • what's the difference between red lines and white lines in gridding?

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    S
    Thank you for the great explanation.
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    C
    Hi In Sim4Life the tissue properties are provided as a single values. However, the IT’IS website provides supplemental information on the tissue properties. In addition to the average value, you can find the standard deviation, minima and maxima. Low Frequency (Conductivity) » IT'IS Foundation](https://itis.swiss/virtual-population/tissue-properties/database/low-frequency-conductivity/)
  • Question Regarding Temporal Interference Tutorial in Sim4Life

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    A
    Dear ZMT Team, I am currently studying the Temporal Interference tutorial with the SAM Head model, as provided in the Sim4Life documentation (Tutorials/EMLF/LF_Multiport.html#temporal-interference-with-sam-head). I have followed the steps carefully up to the solver stage. However, during the simulation run, I encountered the following warning: Solid X_Electrode (Selected_Electrode): PEC - no edges associated with this material and thus it is disregarded. Also, I’m not sure if the simulation problem affects the analysis. The E-field distribution doesn’t show up, but the tutorial shows it in the figure at the bottom. Could you kindly advise if this warning affects the simulation output, and how I might resolve the issue or verify my results? Thank you very much for your time and support.
  • Solver Error in EM-LF Simulation on Yoon-son Model

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  • Jobs suddenly remain queued indefinitely

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    P
    After a call with S4L support, here is the solution for future reference: My machine had two GPUs connected, one of them old and deactivated. However, the script ExtractCudaInfo.py detected both of these in the line 'num_gpus = int(xml_root.find("attached_gpus").text)' and then got stuck trying to find information on the deactivated GPU. A quick fix for the issue is therefore to manually set the correct number, in my case 'num_gpus=1', in the script.
  • High Field Values at Extremities

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    Hi @bryn, I think you’re right. The issue appears to be related to the boundary conditions on the outer bounding box. I changed the boundary to a flux(0) condition, and that resolved the problem with the localized high field values at the extremities. Thank you!
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  • "wire radius"

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    brynB
    Please give more context. E.g., "in the modeler when I use tool X", or in a "Y simulation" there is an option. or in this other thread (link) I asked about Z Then it will be easier to answer your question.
  • Yoon-sun Arm Stimulation Neuron Tutorial Project Compatibility Issue

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    C
    Are you able to run other NEURON tutorials (the pre-build versions)? If not then this issue could be related to the NEURON installation or version. It is possible that using an older version of the NEURON solver is causing the error you mentioned. Please make sure you have the correct version of NEURON installed in your Sim4Life folder. For instance, as you are using Sim4Life version 8.2.0.16876, you should download NEURON using NEURON_setup_8.2.0.16876.exe.
  • Modulated source in thermal simulation

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    @Sylvain Hi, thank you for your reply. I changed modulated field to El. Loss Density and everything works.
  • Thermal, unable to write input files.

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    Thank you. Uploaded.
  • MQS solver errors

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    sending you an email via support
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  • This topic is deleted!

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  • How to get inhomogeneous B0 maps

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  • Simulation outputs

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    Great! Goit it, thank you so much. One last question regarding where the simulation outputs are located and saved. The coordinates of the voxelized entities where can be found? Thank you so much for your time :)
  • White matter anisotropy

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    @bryn Thanks, I found it!
  • Unable to start simulation: failed to write input files.

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    ofliO
    Hi @tayjiekai sim4life.lite is the student version of our online simulation platform sim4life.science and comes with certain limitations. As indicated by the error message, it does not support a number of neurons exceeding 10. If the limitations of sim4life.lite are too restrictive for your work, I suggest transitioning to the full Sim4Life web version at sim4life.science.
  • EM FTDM simulation

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    H
    Joule heating sources from various processes (e.g., EM energy deposition by ohmic losses) can be considered as inhomogeneous heat sources in thermal simulations. To create heat sources Simulation Link: Sensor settings of an EM FDTD simulation in the same project can then be dragged and dropped into Source Settings folder. Modulated Analysis/Cache: Data Origin Type can be defined as: (a) Cache File: select the path of a thermal source previously exported into a .cache file. (b) Analysis Output: select the energy density of interest directly from the Analysis. You can look into the heated brain tutorial for a simplified example.