outputs documentation

[danieljdenman]

hi devs - first, thanks for the open source tool! we (@psharm5) are excited to use it for our project.

working through the examples/tutorial has been helpful for starting (especially ossdbs_tutorial.ipynb) but we are having trouble understanding the outputs, especially of the final run of the volume model. what outputs get saved outside of the notebook and how do we understand the contents of those outputs? some docs on that or just more info in the markdown of the ipynb would be very very helpful.

[j-zimmermann]

Hi Daniel,
Thanks for reaching out!
We haven't yet prepared a first release because we are still testing the code. In this scope, some of the output files changed. We will document the code more extensively once we reach a stable state (hopefully very soon).
For now, I could help you with specific requests. What do you want to look at? And are you interested in frequency- or time-domain results.

I saw that you cloned the repo and pushed it again on GitHub.
To stay up-to-date, I'd recommend you to fork it instead through GitHub.
In this way, you can sync the repositories with one click and also help us with pull requests (if you add new features, for example).

Best regards,
Julius

[psharm5]

Hi Julius, Thank you for your message! When we try to generate results in each of the vtu files in the folder everything is null. Let me know if I may provide any more information and thank you for the advice! Paree

…

On Thu, Oct 17, 2024 at 2:07 PM Julius Zimmermann ***@***.***> wrote: Hi Daniel, Thanks for reaching out! We haven't yet prepared a first release because we are still testing the code. In this scope, some of the output files changed. We will document the code more extensively once we reach a stable state (hopefully very soon). For now, I could help you with specific requests. What do you want to look at? And are you interested in frequency- or time-domain results. I saw that you cloned the repo and pushed it again on GitHub. To stay up-to-date, I'd recommend you to fork it instead through GitHub. In this way, you can sync the repositories with one click and also help us with pull requests (if you add new features, for example). Best regards, Julius — Reply to this email directly, view it on GitHub <#57 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AU7AX6TWOA3FELOWFV5WHVDZ374FJAVCNFSM6AAAAABP5SG25WVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMRQGIYDOOBQGE> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[j-zimmermann]

Hi Paree,

That sounds like a wrong boundary condition setting.
Can you please provide the JSON input file?

Best ,
Julius

[psharm5]

Sure! Let me know if I can provide anything else! Thanks for your help:)

…

On Sun, Nov 3, 2024 at 12:54 PM Julius Zimmermann ***@***.***> wrote: Hi Paree, That sounds like a wrong boundary condition setting. Can you please provide the JSON input file? Best , Julius — Reply to this email directly, view it on GitHub <#57 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AU7AX6URUN7DVTBCQGYHKVTZ6ZPMTAVCNFSM6AAAAABP5SG25WVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINJTGUYTAOJVGM> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[j-zimmermann]

You're welcome but I cannot see the JSON file or the input settings that you chose.
Could you please add it?

[psharm5]

Does this one work? Message ID: ***@***.***>

…

[j-zimmermann]

I can only see your message, no attachments, nothing else.
Please follow the instructions here: https://docs.github.com/en/get-started/writing-on-github/working-with-advanced-formatting/attaching-files
If a JSON file cannot be attached, paste its content into the comment box and format it as code.

[psharm5]

Oh i see my mistake- I was trying to send through gmail but I am attatching here on github thank you for your patience.

`{
  "BrainRegion": {
    "Center": {
      "x[mm]": -9.48,
      "y[mm]": 11.61,
      "z[mm]": 4.68
    },
    "Dimension": {
      "x[mm]": 40.0,
      "y[mm]": 40.0,
      "z[mm]": 40.0
    },
    "Shape": "Sphere"
  },
  "Electrodes": [
    {
      "Name": "BostonScientificVercise",
      "PathToCustomParameters": "",
      "Rotation[Degrees]": 0.0,
      "Direction": {
        "x[mm]": 0.0,
        "y[mm]": 0.0,
        "z[mm]": 1.0
      },
      "TipPosition": {
        "x[mm]": -9.48,
        "y[mm]": 11.61,
        "z[mm]": 4.68
      },
      "Contacts": [
        {
          "Contact_ID": 1,
          "Active": true,
          "Current[A]": 0.004,
          "Voltage[V]": 0.0,
          "Floating": false,
          "SurfaceImpedance[Ohmm]": {
            "real": 0.0,
            "imag": 0.0
          },
          "MaxMeshSizeEdge": 0.05
        },
        {
          "Contact_ID": 2,
          "Active": true,
          "Current[A]": -0.004,
          "Voltage[V]": 0.0,
          "Floating": false,
          "SurfaceImpedance[Ohmm]": {
            "real": 0.0,
            "imag": 0.0
          },
          "MaxMeshSizeEdge": 0.05
        }
      ],
      "EncapsulationLayer": {
        "Thickness[mm]": 0.0,
        "Material": "Blood",
        "DielectricModel": "ColeCole4",
        "MaxMeshSize": 0.1
      }
    }
  ],
  "MaterialDistribution": {
    "MRIPath": "Butenko_segmask.nii.gz",
    "MRIMapping": {
      "Unknown": 0,
      "CSF": 1,
      "White matter": 2,
      "Gray matter": 3,
      "Blood": 4
    },
    "DiffusionTensorActive": false,
    "DTIPath": ""
  },
  "DielectricModel": {
    "Type": "ColeCole4"
  },
  "Mesh": {
    "LoadMesh": false,
    "MeshElementOrder": 2,
    "MeshingHypothesis": {
      "Type": "Fine",
      "MaxMeshSize": 1
    },
    "MeshSize": {
      "Edges": {},
      "Faces": {},
      "Volumes": {}
    },
    "SaveMesh": false
  },
  "EQSMode": false,
  "FEMOrder": 2,
  "StimulationSignal": {
    "CurrentControlled": true,
    "Type": "Multisine",
    "ListOfFrequencies": [
      10000.0
    ]
  },
  "Solver": {
    "Type": "CG",
    "Preconditioner": "bddc",
    "PreconditionerKwargs": {},
    "PrintRates": true,
    "MaximumSteps": 200,
    "Precision": 1e-8
  },
  "PointModel": {
    "Pathway": {
      "Active": false,
      "FileName": ""
    },
    "Lattice": {
      "Active": false,
      "Center": {
        "x[mm]": 10,
        "y[mm]": 10,
        "z[mm]": 10
      },
      "Shape": {
        "x": 10,
        "y": 10,
        "z": 10
      },
      "Direction": {
        "x[mm]": 0,
        "y[mm]": 0,
        "z[mm]": 1
      },
      "PointDistance[mm]": 1
    }
  },
  "OutputPath": "ResultsCC",
  "ComputeImpedance": true,
  "ExportVTK": true,
  "ExportElectrode": true
}
`

[j-zimmermann]

Thanks, that helps to understand your problem.
Please update your local OSS-DBS version to the latest commit on main and adjust the voltage of one of the contacts to a non-zero value.
We have updated the interface for current-controlled stimulation (documentation will come soon, hopefully, we are still testing things).

Then, you should be able to see a non-zero field and potential.