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[edit] Using the 3D Window

3D Window
  • Open a Volume / Gray view Window | Open Volume 3-view Window.
  • Ensure the map is xformed from your inplane data (open an Inplane window, then use the 'Xform' menu in the Volume View.)
  • Open a 3D Mesh Window: Window | Open 3D Window (last option).
  • To build or load a mesh:
    • Building a mesh: In the 3D Window, select File | Build Mesh | (left, right, or both hemsipheres). You may be asked to confirm the selection of white-matter classification file (.class file) before proceeding. A mesh with nominal vertex relaxation ("smoothing" or "inflating") will be created, and you will be prompted to save it.
    • Loading a mesh: In the 3D Window, select File | Load (anatDir). The code will look in some default directories, relative to your Anatomy directory (i.e., the one with the vAnatomy.dat file). These could be [anatomy]/Meshes or [anatomy]/Right/3DMeshes/ or [anatomy]/Left/3DMeshes/. (Or else navigate to the file.)

Now you can overlay data on the mesh.

  • Selecting data to overlay: the 3D Window interfaces between the mrVista VOLUME view and the currently-selected mesh. To overlay data, you need to load it in the selected Volume window. E.g., to view phase data, select View | Phase map in that window. Set the thresholds to what you would like the mesh display to reflect.
  • Press the 'Update' button on the window to display the overlay in the currently-selected Volume window on the mesh. The mesh will inherit the color map, thresholding, and ROI display preferences from this view.
  • To view ROIs only, select Mesh | Anat / ROIs. This will set both the Volume and mesh to display ROIs, absent any overlays that may be loaded into the Volume view.
    • Similarly, you can select Mesh | Phase, Map, Co, or Amp to set both the view and mrMesh to the relevant data display mode. Note, however, that the data should already be loaded into the Volume view before you can display it.
    • Note also that the display of ROIs on the mesh is contingent on the Volume view's ROI settings: it can display only the selected ROI, display all ROIs, or hide the ROIs; and it can draw a filled ROI (equivalent to drawing boxes around each pixel in the Volume view) or an ROI outline. To modify these settings in the Volume view, select the menu ROI | Hide/Show ROIs | Set ROI Preferences (Ctrl+3).
    • Further finer points about ROIs: the mesh preferences, set using the command line mrmPreferences or the menu Edit | Preferences..., may also influence how data and ROIs are displayed. The roiPerimThickness preference may thicken ROI outlines (if you select the show outline option). The layerMapping affects the layers from which data are drawn. For higher-resolution data, the gray matter at a given location may map to multiple voxels in the data (b/c of the thickness of the gray matter). Selecting 'layer1' restricts both data and ROIs to the first gray level above the white matter. Selecting 'all' does something more complex. The mapping now depends on the 'layerMapMode' [sp?] preference. If this value is set to 'mean', the plotted data reflect the mean across all gray matter voxels which map to a particular point on the mesh. If it is set to 'max', it takes the maximum value. In both cases, the ROI is plotted as an OR function of these voxels: if any of the gray voxels which map to the mesh point are contained within the ROI, the mesh is colored to reflect that the ROI is there.
    • [more fine points about how the 'all' mapping is computed, branching through all connected edges]

The smoothing level is set using 'Smooth Mesh (set options)'. To get a large level of inflation, as typically seen in BrainVoyager/Freesurfer meshes, set the smooth level to around 1.2 and the relaxation iterations to about 128.

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