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ZMT zurich med tech

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  4. Error in TI tutorial

Error in TI tutorial

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  • A abbytang

    When I restart the software and only import IXI025-Guys-0852-T1.nii.gz, the auto-label function works correctly.

    However, when I run tutorial_TI_|X|025_head_model.ipynb, the same error occurs again.

    After the error occurs, if I only load IXI025-Guys-0852-T1.nii.gz and run the 'auto-label function' (head modeling in the Ribbon), the same error now appears at this step. The only way to resolve it is to restart the software and reload IXI025-Guys-0852-T1.nii.gz—then it works correctly again.

    However, if I try to run the TI tutorial, the error persists even after restarting the software.

    image.png

    ![0BB7M7UAW`1BYC63FR)U]26.png](/assets/uploads/files/1748234490112-b021ff28-75cd-48f4-a814-49a0e4042b11-0bb7m7uaw-96-1byc63fr-u-26.png)

    brynB Offline
    brynB Offline
    bryn
    ZMT
    wrote last edited by
    #7

    @abbytang Thanks for the update. We will try to reproduce the issue, and if possible either provide a workaround or contact you to understand why it happens.

    Can you run other tutorial notebooks, e.g. the mesh extrusion tutorial?

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    • A Offline
      A Offline
      abbytang
      wrote last edited by
      #8

      Thank you for your reply. The mesh extrusion tutorial runs correctly. Since my research focuses on TI, I need tutorial_TI_|X|025_head_model to run correctly. I would greatly appreciate any assistance with resolving those issues.

      image.png

      image.png

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      • brynB Offline
        brynB Offline
        bryn
        ZMT
        wrote last edited by
        #9

        Are you using the latest Sim4Life, v8.2.2.18061?

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        • A Offline
          A Offline
          abbytang
          wrote last edited by
          #10

          Yes, I'm currently using the latest Sim4Life version (v8.2.2.18061). I will also install version 8.2.0.16876 and test it again for comparison.

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          • A Offline
            A Offline
            abbytang
            wrote last edited by
            #11

            When I copy the file tutorial_TI_|X|025_head_model.ipynb into the CAD files folder of Sim4Life version 8.2.0.16876 and run it in this older version, most sections execute correctly, including the "Auto Label Tissues and Extract Surfaces" part. However, the script fails at the "Computing the Maximum Modulation Using the Masked Electric Fields" section with the following error:
            AttributeError: module 's4l_v1.analysis.core' has no attribute 'MaxModAmpEvaluator'.
            Could you please advise on how to resolve this issue? Thank you for your assistance.

            image.png

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            • brynB Offline
              brynB Offline
              bryn
              ZMT
              wrote last edited by
              #12

              the MaxModAmpEvaluator was exposed in s4l_v1 6 months ago, so after 8.2.0.16876. You could probably use it though via the 'raw api': XPostProcessor.MaxModAmpEvaluator.

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              • brynB bryn

                The error looks like something is wrong with the matplotlib package in your installation (the MPLBACKEND environment variable). Did you possibly install any python packages in Sim4Life's Python with 'pip'?

                Can you run any other notebooks with matplotlib plots?

                L Offline
                L Offline
                lucky_lin
                wrote last edited by
                #13

                @bryn Hello, I am using a script to run TI simulations. I noticed that when I change the maximum grid step size for the electrodes and tissues from [2.0, 2.0, 2.0] to [3.125, 3.125, 3.125] in each simulation, the peak value of the calculated electric field (E-field) changes from 205 V/m to 445 V/m. Why does the grid step size affect the final calculated E-field value? Additionally, I found that changing the step size also significantly alters the Scale Factor used to normalize the results in each simulation. Here is the relevant code :
                manual_grid_settings.MaxStep = numpy.array([3.125, 3.125, 3.125]), units.MilliMeters
                manual_grid_settings.Resolution = numpy.array([1.0, 1.0, 1.0]), units.MilliMeter
                26caa43b-1a9f-471a-bcac-c9f094e6b7ac-f7133268edf385e3629f1eb84541ed1.jpg
                56231949-d3bd-42c7-8b1a-da663561de5e-c6a39d9569d9d76c852280466adfcea.jpg

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                • brynB Offline
                  brynB Offline
                  bryn
                  ZMT
                  wrote last edited by
                  #14

                  @lucky_lin Please post your question as a separate thread. This is unrelated to the topic of this thread. Thanks

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                  • brynB Offline
                    brynB Offline
                    bryn
                    ZMT
                    wrote last edited by
                    #15

                    @abbytang I can reproduce your issue in v8.2.2.18061. Investigating what is causing it and what workaround i can offer (except for reverting to the previous version). Sorry for the inconvenience.

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                    • A Offline
                      A Offline
                      abbytang
                      wrote last edited by
                      #16

                      Thank you for your help. I will run it in a previous version.

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