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I am going over an example from ami.js https://github.com/FNNDSC/ami/blob/dev/examples/viewers_quadview/viewers_quadview.js to visualize a 2D slice of a 3D model of a bone overlayed as a segmentation mask over a 2D image of a corresponding CT scan.

The only difference is that I modified it to read the 3D model mesh from a STL file instead of freesurfer.

The problem is that it renders artifacts of the segmentation mask from previous slices on top of the current CT scan. Instead of rendering a mask corresponding to the current CT scan.

In order to visualize the slices of the 3D model as 2D segmentation mask over 2D CT scans, the example creates a plane corresponding to the 2D slice with the CT scan. 

function updateClipPlane(refObj, clipPlane) {
  const stackHelper = refObj.stackHelper;
  const camera = refObj.camera;
  let vertices = stackHelper.slice.geometry.vertices;
  let p1 = new THREE.Vector3(vertices[0].x, vertices[0].y, vertices[0].z)
  .applyMatrix4(stackHelper._stack.ijk2LPS);
  let p2 = new THREE.Vector3(vertices[1].x, vertices[1].y, vertices[1].z)
  .applyMatrix4(stackHelper._stack.ijk2LPS);
  let p3 = new THREE.Vector3(vertices[2].x, vertices[2].y, vertices[2].z)
  .applyMatrix4(stackHelper._stack.ijk2LPS);

  clipPlane.setFromCoplanarPoints(p1, p2, p3);

  let cameraDirection = new THREE.Vector3(1, 1, 1);
  cameraDirection.applyQuaternion(camera.quaternion);

  if (cameraDirection.dot(clipPlane.normal) > 0) {
    clipPlane.negate();
  }
}

and applies it to the 3D mesh as a clipping plane during rendering

function render() {
  ... some code ...

  // render r2 view
  r2.renderer.clear();
  r2.renderer.render(r2.scene, r2.camera);
  // mesh
  r2.renderer.clearDepth();
  data.forEach(function(object, key) {
    object.materialFront.clippingPlanes = [clipPlane2];
    object.materialBack.clippingPlanes = [clipPlane2];
  });
  r2.renderer.render(sceneClip, r2.camera);

  ... some code...
}

jsfiddle that illustrates the problem is here http://jsfiddle.net/crfs6ugq/226/

user3560320
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  • I don't understand what the problem is. I don't know what a "segmentation mask" is. What am I looking for in your fiddle? It looks cool to me.. :) – manthrax Sep 26 '18 at 10:01
  • I fixed your vertex normal calc so the gooey bits don't look as polygonal :) (by converting to regular geometry and merging vertices before calculating normals ) http://jsfiddle.net/manthrax/248udpkt/8/ – manthrax Sep 26 '18 at 10:11
  • @manthrax the 2D views show a CT scan with a purple colored segmentation mask and white colored bones. They will change as you scroll over any of them, meaning you will go over all slices that are loaded. The problem is that the purple color is lagging behind the white one, which is wrong. The purple color should be in the position of the white colored bones. The code I posted above shows how the mesh corresponding to the purple color is updated. It's quite hard to understand it without being familiar with ami.js. – user3560320 Sep 26 '18 at 13:19

0 Answers0