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  1. The Virtual Brain
  2. TVB-1227

Update documentation for Connectivity Section

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    Details

    • Type: Task
    • Status: Closed
    • Priority: Critical
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: 1.1.1
    • Component/s: None
    • Labels:
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      Description

      Mention about the Connectivity Space-Time screen should be made in the UserManual!!!

      I was thinking that I should update the documentation with this long example and extend a bit what you already wrote. Otherwise it's information that will remain hidden.
      Also, I came across another example of 'bulk' edge operation that will be extremely useful to have: setting the diagonal elements to a certain value.
      Many structural matrices have them and some other do not. It depends on the tractography reconstruction algorithm.
      In the case these connections (aka self-connections) are present, some modelers choose to set them to zero depending on the model and some other assumptions they make.

      I asked Lia about this and she showed me a way to achieve what you need. It's good to know that I can always learn a bit more about TVB.
      This functionality was not completely clear, so the documentation has been updated and we'll try to improve it to accommodate more interesting cases.

      Bulk operations are available for both nodes and edges. Based on what Lia told me:

      *HOW TO ELIMINATE INTER-HEMISPHERIC CONNECTIONS

      + Select multiple nodes from the Connectivity

      <Connectivity_SelectASetOfNodes.png>

      + Apply the changes. The selected nodes appear in green.

      <onnectivity_SelectASetOfNodes_b.png>

      + Save the selection to make it easier later.

      <Connectivity_SaveSelection.png>

      + The Connectivity editor will be aware of two sets of nodes: the ones in your selection (green nodes) and the ones that are not selected (white nodes).
      + Move to the third quadrant (Q3) for instance. I zoomed the 3D visualizer to show the interhemispheric connections
      <Connectivity_ShowConnections.png>

      + Then you can proceed to perform some operations on the edge values, namely: set, add, multiply, divide or subtract.
      <Connectivity_EdgeOperations.png>

      There are four categories of edges depending the nodes they connect:

      • edges IN-IN. These edges connect pair of nodes in the selected set. (In this particular case you would modify the edges from the left hemisphere)
      • edges OUT-OUT. These edges connect pair of nodes in the 'unselected set'. (In this case they would be the right intrahemispheric edges)
      • edges IN-OUT. These are the edges that connect nodes in the selected set (rows) to nodes in the unselected set (columns). (In this case it refers to the edges in quadrant 2)
        + Select operation "Set" for edges "IN-OUT", set the value to 0 and then press button Apply

      <Connectivity_SetInOut.png>

      • edges OUT-IN. These edges connect nodes in the unselected set (rows) to nodes in the selected set (columns). (In this case it refers to the edges in quadrant 3)
        + Select operation "Set" for edges "OUT-IN", set the value to 0 and then press button Apply

      <Connectivity_SetOutIn.png>

      The interhemispheric connections have disappeared:

      <Connectivity_NewMatrix.png>

      + Save your new matrix

      <Connectivity_SaveNewConenctivity.png>

      Once you have your new matrix, you can launch the connectivity visualizers and check that these connections are not there any more.

      <Connectivity_ReloadView.png>

        Gliffy Diagrams

          Attachments

          1. Connectivity_EdgeOperations.png
            Connectivity_EdgeOperations.png
            470 kB
          2. Connectivity_NewMatrix.png
            Connectivity_NewMatrix.png
            605 kB
          3. Connectivity_ReloadView.png
            Connectivity_ReloadView.png
            581 kB
          4. Connectivity_SaveNewConenctivity.png
            Connectivity_SaveNewConenctivity.png
            600 kB
          5. Connectivity_SaveSelection.png
            Connectivity_SaveSelection.png
            107 kB
          6. Connectivity_SelectASetOfNodes.png
            Connectivity_SelectASetOfNodes.png
            420 kB
          7. Connectivity_SetInOut.png
            Connectivity_SetInOut.png
            413 kB
          8. Connectivity_SetOutIn.png
            Connectivity_SetOutIn.png
            409 kB
          9. Connectivity_ShowConnections.png
            Connectivity_ShowConnections.png
            596 kB
          10. onnectivity_SelectASetOfNodes_b.png
            onnectivity_SelectASetOfNodes_b.png
            422 kB

            Activity

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              Assignee:
              paula.sanz-leon Paula Sanz Leon
              Reporter:
              paula.sanz-leon Paula Sanz Leon
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