MenuGray

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  • Open a Volume / Gray view.
  • Ensure the map is xformed from your inplane data (open an Inplane window, then use the 'Xform' menu in the Volume View.)
  • To build or load a mesh:
    • Building a mesh: select Gray | Surface Mesh | 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: select Gray | Surface Mesh | Load Mesh or use the shortcut Ctrl-comma. 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.

  • Ensure the data are loaded and displayed in the Volume/Gray window.
  • Select Gray | Update Mesh (shortcut: Ctrl-zero (0)) 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.
    • Note 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).
    • The mesh preferences, set using the command line mrmPreferences or the menu Gray | Mesh Display Tools | Mesh Preferences (shortcut: Ctrl-period), 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. DataSmoothIterations is the # of surface-based data smoothing iterations. 0 does no smoothing. On each iteration, the data for each node is replaced with the mean of its neighbors. We usually do 1 or 2 just for aesthetics when making an image. For a serious analysis, you probably want no smoothing (0). RoiDilateIterations is the # or ROI dilation iterations. I don't remember the specific algorithm, but I think it's similar to data smoothing but for the ROI. I usually keep this at 0. ClusterThreshold is experimental. I think it will avoid rendering data blobs with fewer than this many connected voxels in the gray nodes. E.g., if this is 10 then any blobs of data with fewer than 10 connected gray nodes won't be shown on the surface. It can reduce the 'speckle' of noise blobs on the surface. Again, I just play with this to make nice visualizations. If I were doing a careful analysis, I'd leave it off (set to 0).
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