3D visualization of the brain. Jean-Marc Gauthier www.tinkering.net

The brain project: 3D visualization and navigation
Patrick J Kelly, MD FACS NYU and Jean-Marc Gauthier ITP Tisch School of the Arts NYU

Collaborators for this project also include ITP student members of the Brain Group: Caroline Pino, Rocio Barcia, Jae In Lee, Sandra Villareal, Chunxi Jiang.

"Kelly and Gauthier's new Internet-based Web browser allows 3-D navigation inside a brain using a cloud of voxels, or pixels, located in space. Since the images of slices of the brain are displayed in space they can be visited from many angles, including new angles that were not included in the original pictures. This is key to enabling freer navigation. The viewer can then navigate the virtual brain in any direction regardless of the orientation of the original slices of the MRI." Read the full article at http://www.nyu.edu/nyutoday/archives/20/04R/Stories/Software-3-D.html

The following steps show how a 3D visualization of the brain can be created from a sequence of MRI images. Source: NYU Medical Center.

1) In this example, we use six MRI images of the brain taken along the same axis. The images are organized in a sequence of frames that can be viewed as a film strip.


This illustration shows the sequence of MRI images displayed inside a 3D space creating a cloud of pixel-points. The resulting volume is a 3D object with the following material attributes: texture blend = decal, material = transparent. A point-cloud shader is applied to the 3D object.		A visualization plane is now inserted inside the cloud of pixel-points. Real time images of the brain can be viewed on the plane slicer while in motion.

Creating in between frames not included in the original image		Creating new angles not included in the original image
The top view shows the visualization plane moving inside the point cloud object. The plane slicer is aligned with the axis of the sequence of MRI images presented in (1). Bottom view, the point cloud is turned off. Although the plane slicer moves between two frames of the sequence of MRI images, an image is still visible on the plane slicer. This image is the result of the interpolation between two frames of the sequence of MRI images presented in (1).		The top view shows the visualization plane moving inside the point cloud object at an angle. The plane at a 45 degree angle with the axis of the sequence of MRI images. The bottom view shows the plane slicer with the point cloud turned off. Please note that although the plane is at an angle with the sequence of MRI images, an image is still visible on the plane slicer. This image is the result of the interpolation between two frames of the sequence of MRI images presented in (1).

This illustration shows the sequence of MRI images displayed inside a 3D space creating a cloud of pixel-points. The resulting volume is a 3D object with the following material attributes: texture blend = decal, material = transparent. A point-cloud shader is applied to the 3D object.

A visualization plane is now inserted inside the cloud of pixel-points. Real time images of the brain can be viewed on the plane slicer while in motion.

Creating in between frames not included in the original image

Creating new angles not included in the original image

The top view shows the visualization plane moving inside the point cloud object. The plane slicer is aligned with the axis of the sequence of MRI images presented in (1). Bottom view, the point cloud is turned off. Although the plane slicer moves between two frames of the sequence of MRI images, an image is still visible on the plane slicer. This image is the result of the interpolation between two frames of the sequence of MRI images presented in (1).

The top view shows the visualization plane moving inside the point cloud object at an angle. The plane at a 45 degree angle with the axis of the sequence of MRI images. The bottom view shows the plane slicer with the point cloud turned off. Please note that although the plane is at an angle with the sequence of MRI images, an image is still visible on the plane slicer. This image is the result of the interpolation between two frames of the sequence of MRI images presented in (1).