Tips

June 2003 - Issue 18
E-Newsletter for Tecplot Users

04.  TECPLOT TIPS - VOLUME GENERATION FROM 2-D MRI SLICES

In Step 1 we loaded the MRI slice data into Tecplot. In Steps 2 and 3 we concatenate the slice data and generate a 3-D image of the brain.

Step 1: Editing the Data File
1. Open output2d.dat (14,451 KB) created in Step 1 with a text editor.
The text file includes variables I, J, K and intensity ("V5").
The 10 zones are flat 2-D slices (186 by 226) with intensity at each location.

2. The goal is to combine the 10 individual zones into one 3-D zone.
Change K from 1 to 11. (We want 11 K planes in one zone versus 1 K plane in 11 zones).

3. Copy and paste ZONE T into the text editor's Find tool.

4. Find the next Zone T.
(Notice how the K-value is 3, 6, 9... as a result of changing the slice distance from 1 to 3 units in Step 1 .)

5. Delete the entire zone header for each remaining zone. (Keep the fist header where K=11.)
Save the file.

Step 3: Visualizing in 3-D
1. Load the edited output2d_modified.dat file back into Tecplot.
The new file has about about 500,000 points in ASCII format. Tecplot will convert the file to binary.

2. Turn off Mesh and turn on Contour.
Make V4 : V5 (intensity) the Contour variable.
The IJK-ranges and brain are now visible.

3. View the brain's top and bottom by rotating the volume with the Roller-ball tool.

4. Open the Value Blanking dialog. Activate blanking when V4 : V5 (intensity) is less than or equal to zero.
This will eliminate the blue region of the volume.

5. After blanking, the plot looks like a skull with the top sheered off.

6. Turn off Contour.
With the 3D Slice Detail dialog, place two slices in the Z-direction.

7. Using the Slice tool, interactively move a slice up and down the volume.

8. Open the Animate Slices dialog (Tools/Animate/Slices). Change the number of slices to 50.
Click Animate.
You can view animations on screen (similar to these examples) or optionally export an AVI animation.

9. Using the Color Map dialog (Workspace/Color Map), view the plot in grayscale. Grayscale will make the image look similar to an actual MRI.
(Depending on the type of analysis you are doing, you can apply custom color maps to make your data look more life like.)

10. Use the 3D Iso-Surface Details dialog to add one iso-surface at an intensity of 63.75.

11. With the iso-surface activated, the skull and brain are visible.

12. Using a combination of iso-surfaces, slices and different color maps you can develop several different plots for analysis or presentation.

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