SkullStrip.vqs

After selecting a seed point, this script uses the 3D ROI Spline Tool for skill stripping a brain data set slice-by-slice.

/**
 * Script for skull stripping a brain data set slice-by-slice using
 * the 3D ROI Spline Tool in VivoQuant.  User only has to select a
 * seed point and QA the results at the end.
 *
 * Author: Gabriel Tobon <tobon@invicro.com>
 */
 
// GLOBAL VARIABLES
var DM = VQ.dataManager();
var MW = VQ.mainWin();
var VC = VQ.controler();
 
function main()
{
    MW.setViewMode("Slice View", "3D ROI Tool");
    var roiOp = VQ.currentOp();
    
    // Delete all current ROIs and create a "Brain ROI"
    var ids = [];
    var numROIs = roiOp.numROIs();
    for (var i=1; i < numROIs; ++i) ids.push(i);
    if (ids.length > 0)
    {
        roiOp.deleteROIs(ids, 0);
    }
    roiOp.addROI("Brain", "red");
    roiOp.setCurrentROI(1);
 
    // Activate spline mode
    VQ.getWidget("tabWidget").setCurrentIndex(2);
    roiOp.setModeSplineIsocount();
    VC.setPos(2, 0);
    
    // Ask for seed point
    VQ.suspend("Please select a seed point and threshold");
 
    // Iterate through slices, computing percentile threshold
    // and applying that threshold to generate the mask
    for (var z=0; z < DM.getDimZ(); ++z)
    {
        roiOp.acceptedSplineNext();
    }
 
    // Display Message
    VQ.showMessage("VivoScript complete! Please QA and adjust the brain mask as needed");
}
 
main();