LABORATORY OF NEURO IMAGING 3D VISUALIZATION TOOL

LONI Visualization Tool (LONI_Viz)®

Surfaces and 3D Volume Rendering Models using LONI_Viz®

LONI_Viz allows the display of 3D cortical models saved as LightWave (*.lwo & *.lws) objects. A LightWave Scene can be loaded in using Display-->Display 3D Surface Model. For now an external program must generate the LightWave Object (*.lwo) file. The Scene file (*.lws) can be created using any of the ASCII scene files we provide in the "data.dir" directory, by updating the LWO file name on line 12 (LoadObject OLD_LWO.lwo). In the near future we will allow the user to create LWO surface objects, online from within LONI_Viz, either at a fixed iso-value or from a series of concentric (cross-plane) manually drawn contours. The details of the surface generation, triangulation, normalization, etc. are still in development.

The current LightWave loader class correctly loads only LWO objects version 5 and lower, not 6+. Perhaps, this would change as the new 6+ version is improved and debugged. To use the full capabilities of the LONI_Viz 3D viewer you would need to have Java 3D media installed on your machine (this doesn't come by default with the Java compiler/interpreter). You can download and quickly install these additional packages by going to Java 3D. It is amazing how good and fast the Java 3D visualization is once one has the LWO object files.

Below are two examples of the 3D surfaces of a human and a mouse brain displayed by LONI_Viz

Here is the protocol for generating surface models using the manually drawn MCF contour files:

Refine the MCF contours: This step simply attempts to resolve small loops and self-intersections within each contour in the MCF. The output should be a list of simple-closed-curves;
- java edu.ucla.loni.LONI_Viz.FixSelfIntersectedMCF MAP_Contour_original.mcf fixed_MAP_Contour_original.mcf
Convert the single ROI MCF --> CNT file
- java edu.ucla.loni.LONI_Viz.MCF_to_CNT MAP_contour_Cerebellum.mcf > MAP_contour_Cerebellum.cnt
- Note of caution: Even though "MCF_to_CNT" attempts to resolve certain inconsistencies with the manually drawn contours, depending on the painter, one may need to repeat the following process to get rid of self-intersections of the contours. Topologically correct surfaces require simple-closed-contours! If the output of the next step (nuages) generates errors indicating self-intersecting contours you will need to inspect the contours where problems arise. One way to do this is to cut-and-paste the problem contour in a file "gnuplot_data.dat". Then call "gnuplot", interactive plotting program, and within gnuplot type load "gnuplot.help". This will plot the problematic contour and you can visually inspect the problem points where the contour self-intersects. Remove, or adjust, these points in the CNT file and re-try nuages, below. You may need to do this several times to resolve all non-simple contours for a given CNT file. Almost exclusively problems arise at the begining or the end of the contour, or sometimes when a line segment sticks out by itself. These are easily identifyable by visual inspection of the "gnuplot" 2D plot.
Generate a DXF surface file:

/loni/map/MAP/Mouse15/MRI/IMG/MCF_2_DXF.dir/NUAGES_SGI/bin/nuages MAP_contour_Cerebellum.cnt -dxf -tri MAP_contour_Cerebellum.dxf
Open LW/LWM and load the DXF file, make adjustments, create a scene and export/output it as a LightWave Scene (*.lws) file and a LightWave Object (*.lwo) file.