ZMT zurich med tech

thanks for this feedback. we will try to add more examples that demonstrate how to use/modify anatomical models, triangle meshes, etc.

I ended up creating my Duke model in a separate script, where I first cloned him as static. Then I removed part of the body not relevant to me by boolean subtraction (entity by entity) and finally export the remain static model to a sab file, which I load in my main script instead of the entire Duke. It has been this confusion about entities and groups and what not disturbing the flow. Thanks for your suggestions bryn

I tried to reproduce this doing the following. I create three entities a cylinder copy it and convert the copy to a triangle mesh generate an unstructured tetrahedral mesh Then I drag these entities to the Analysis (ModelToGridFilter in Python API). I tried to use the surface viewer, but since they have no fields, nothing is displayed (this changed since 7.0 or before - it used to display a white surface). To generate a field I used the Calculator, and added expressions like coordsY*jHat, i.e. (0, coordsY, 0) where coordsY is the y-coordinate from the points in the geometry. Create a vector viewer for each (from the left: Solid Body, TriangleMesh, UnstructuredMesh). The third one samples vector values using Line/Plane/Box sources. [image: 1749109986009-d5bc2f0e-af54-4fca-8265-1431e94207ca-image.png] To get the vectors on the surface of the UnstructuredMesh, I had to first extract the surface, via Field Data Tools -> Surface Filter [image: 1749110185730-938040d9-2fcf-4cad-a42e-7c2f0d4592ec-image.png] The generated Python ("To Python' in context menu) script for item 5 was: # This script was auto-generated by Sim4Life version 8.2.0.16890 import numpy import s4l_v1.analysis as analysis import s4l_v1.document as document import s4l_v1.model as model import s4l_v1.units as units from s4l_v1 import ReleaseVersion from s4l_v1 import Unit try: # Define the version to use for default values ReleaseVersion.set_active(ReleaseVersion.version8_2) # Creating the analysis pipeline # Adding a new ModelToGridFilter inputs = [] model_to_grid_filter = analysis.core.ModelToGridFilter(inputs=inputs) model_to_grid_filter.Name = "Cylinder 3" model_to_grid_filter.Entity = model.AllEntities()["Cylinder 3"] model_to_grid_filter.UpdateAttributes() document.AllAlgorithms.Add(model_to_grid_filter) # Adding a new FieldCalculator inputs = [model_to_grid_filter.Outputs["Unstructured Grid"]] field_calculator = analysis.field.FieldCalculator(inputs=inputs) field_calculator.Expression = u"coordsZ*kHat" field_calculator.UpdateAttributes() document.AllAlgorithms.Add(field_calculator) # Adding a new FieldSurfaceFilter inputs = [field_calculator.Outputs["Result(x,y,z)"]] field_surface_filter = analysis.field.FieldSurfaceFilter(inputs=inputs) field_surface_filter.UpdateAttributes() document.AllAlgorithms.Add(field_surface_filter) # Adding a new VectorFieldViewer inputs = [field_surface_filter.Outputs["Result(x,y,z)"]] vector_field_viewer = analysis.viewers.VectorFieldViewer(inputs=inputs) vector_field_viewer.Data.Phase = u"0°" vector_field_viewer.Vector.Plane.PlaneCenter = numpy.array([0.05300000309944153, -0.03099999949336052, 0.012000000104308128]) vector_field_viewer.UpdateAttributes() document.AllAlgorithms.Add(vector_field_viewer) except Exception as exc: import traceback traceback.print_exc() # Reset active version to default ReleaseVersion.reset() raise(exc)

The voxeler (re-)uses cached information about the geometry (solids, wires, etc.). It looks up the information for each model entity and emits this message if the cached geometry was not found. Questions: are you running this in the GUI or a script/notebook? did you potentially delete (or modify) some of the entities assigned to the simulation (I guess in voxeler settings)? If you deleted the entity or modified it in the modeler (some operations preserve the instance, while others may create a new instance and delete the old one), this would explain the error. We could improve the error message by providing more helpful instructions.

This is in an older version of sim4life 8.0, maybe the problem has already been fixed. Otherwise I think this was a multiport simulation but I forget now... Maybe that could be a strange bug where it works for multi but not single or vise versa.

So my problem was solved for the simple phantom a sphere. It can be voxeled. I am having a discussion with chatgpt about how to load Duke into the simulation section because currently it wont be voxeled. Is there a simple few lines of code that loads Duke and all the default tissue electrical properties or is it necessary to assign each tissue type in a loop or via thousands lines of code (as I have seen elsewhere)....

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.

@Sylvain I exported the electric field results from an AC simulation and found that the last six columns of the data are imaginary numbers. Are these the electric field values in three different directions? Why aren't they time-varying? Did I only export the peak values?

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!

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

To measure the shortest distance between two entities, you can use the Python API: import XCoreModeling as xcm shell = xcm.GetActiveModel().SelectedEntities[0] coil = xcm.GetActiveModel().SelectedEntities[1] res = xcm.GetEntityEntityDistance(shell, coil) print(f"Shortest distance shell-coil: {res[0].Distance}") p1 = xcm.CreatePoint(res[0].ClosestPosition) p1.Name = "Point on Shell" p2 = xcm.CreatePoint(res[1].ClosestPosition) p2.Name = "Point on Coil" # This line is just to visualize where the measured distance was taken line = xcm.CreatePolyLine([res[0].ClosestPosition, res[1].ClosestPosition]) This would create something like this: [image: 1747752108672-c17b7bff-2d64-408c-88a7-fd83a4dadfdb-image.png] Some other snippets are shared here: https://forum.zmt.swiss/topic/565/geometry-modeling-snapping-to-endpoints-in-python-api/3?_=1747746585465

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

Hi, Sorry to bother You. IN ATTACHED VIDEO SHOWS WHAT HAPPENS AFTER CLICKING THE OPTION "CREATE PLOT" AND THE SYSTEM CRASHES. The workstation and memory have been tested, all without errors. Can one of the service engineers help? Kind regards, Thank you, Andrei Andrei Churakov MD,PhD, Associate Professor of the Department of Electronic Engineering and Technology BSUIR E-mail: anchurakov@bsuir.by

This question is quite old. Maybe you found a solution? Otherwise I guess you could use one of these options: you can crop the field, e.g. via the bounding box (or the extent if you have an E-field on a rectilinear grid) you could use the interpolation filter: define your little box grids, and interpolate from the field sensor field to your box grids you could define small field sensors in the simulation setup (not sure it is scalable to hundreds of sensors)

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.

For the unstructured version of the EM LF Electro you would first need to generate a tetrahedral mesh. The mesh can be dragged onto such a simulation.

I would add that in the first approach you might change the tissue property of the original bladder to something else, e.g. fat, to get the desired effect of shrinking or stretching the bladder without creating air holes. Btw, you can measure the volume of a tissue surface in the modeler using the measure tool.

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.

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.