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ZMT zurich med tech

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  4. White matter anisotropy

White matter anisotropy

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  • P Offline
    P Offline
    Pastis
    wrote on last edited by
    #1

    Hello
    i was able to use the trial version of the software and finally we bought it and now we want to perform TI simulation with anisotropic properties of the whitte matter and in the midbrain.
    the 2 screenshot was a simulation performed by Antonino Cassara and i would like to reproduce the simulation he sent us but i don't have access to the anisotropic data.
    how to have access to these files ?

    12.PNG 22.PNG

    brynB 1 Reply Last reply
    0
    • P Pastis

      Hello
      i was able to use the trial version of the software and finally we bought it and now we want to perform TI simulation with anisotropic properties of the whitte matter and in the midbrain.
      the 2 screenshot was a simulation performed by Antonino Cassara and i would like to reproduce the simulation he sent us but i don't have access to the anisotropic data.
      how to have access to these files ?

      12.PNG 22.PNG

      brynB Offline
      brynB Offline
      bryn
      ZMT
      wrote on last edited by
      #2

      @pastis the anisotropic conductivity is subject specific, and could be evaluated from diffusion weighted images (based on Tuch et al.). Sim4life has an implementation to compute this, but we recently noticed a bug in 6.2 which has been fixed for the 7.0 branch. We will include a python tutorial for this workflow in the 7.0 release.

      Alternatively, Sim4Life allows to generate anisotropic conductivity tensor fields given a field that encodes the main directionality (i.e. direction of largest eigenvector). This can be useful for tissues where there is a known directionality, e.g. along some elongated structure.

      G 1 Reply Last reply
      0
      • brynB bryn

        @pastis the anisotropic conductivity is subject specific, and could be evaluated from diffusion weighted images (based on Tuch et al.). Sim4life has an implementation to compute this, but we recently noticed a bug in 6.2 which has been fixed for the 7.0 branch. We will include a python tutorial for this workflow in the 7.0 release.

        Alternatively, Sim4Life allows to generate anisotropic conductivity tensor fields given a field that encodes the main directionality (i.e. direction of largest eigenvector). This can be useful for tissues where there is a known directionality, e.g. along some elongated structure.

        G Offline
        G Offline
        gc00
        wrote on last edited by
        #3

        @bryn I would like to include the white matter anisotropy too, is there a tutorial on how to include DTI?

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        • brynB Offline
          brynB Offline
          bryn
          ZMT
          wrote on last edited by
          #4

          The latest 8.2 release includes a tutorial Jupyter notebook (tutorial_dti_conductivity.ipynb) demonstrating how to import the DTI, convert it to anisotropic conductivity, and assign it to a low-frequency simulation via Python.

          G 1 Reply Last reply
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          • brynB bryn

            The latest 8.2 release includes a tutorial Jupyter notebook (tutorial_dti_conductivity.ipynb) demonstrating how to import the DTI, convert it to anisotropic conductivity, and assign it to a low-frequency simulation via Python.

            G Offline
            G Offline
            gc00
            wrote on last edited by
            #5

            @bryn this is the list of the tutorials that I found in C:\Users\Documents\ZMT\Sim4Life\8.2\Documentation\Tutorials\Tutorial Scripts: tutorial_acoustic_seft
            tutorial_emftd_dipole_antenna_broadband
            tutorial_emftd_dipole_antenna_harmonic
            tutorial_emftd_ieee_scc34_benchmark
            tutorial_emftd_microstrip_fed_patch_ant
            tutorial_emftd_mri_single_loop_coil
            tutorial_emftd_mri_system_and_lead_pa
            tutorial_emftd_plane_wave
            tutorial_emftd_pt3Coil
            tutorial_emftd_SAHeadPhone
            tutorial_emftd_gradient_coil
            tutorial_emftd_parallel_plate
            tutorial_emftd_transcranial_magnetic_stim
            tutorial_emfl_two_metallic_spheres
            tutorial_emfl_unstructured_neuron_electrodes
            tutorial_head_segmentation_10_10_system
            tutorial_neuron_hoc
            tutorial_neuron_monopole
            tutorial_neuron_neural_networks
            tutorial_petri_dish_T1_fields
            tutorial_thermal_heated_brain
            tutorial_tier3_simulation

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            • brynB Offline
              brynB Offline
              bryn
              ZMT
              wrote on last edited by
              #6

              It is a Jupyter notebook:

              C:\Users\Public\Documents\ZMT\Sim4Life\8.2\Documentation\Example Notebooks

              G 1 Reply Last reply
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              • brynB Offline
                brynB Offline
                bryn
                ZMT
                wrote on last edited by
                #7

                You can also find the Example Notebooks via the GUI:

                Youtube Video

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                • brynB bryn

                  It is a Jupyter notebook:

                  C:\Users\Public\Documents\ZMT\Sim4Life\8.2\Documentation\Example Notebooks

                  G Offline
                  G Offline
                  gc00
                  wrote on last edited by
                  #8

                  @bryn Thanks, I found it!

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