Tips

June 2003 - Issue 18
E-Newsletter for Tecplot Users

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

Last month we reviewed 2-D image analysis — specifically how to perform 3-D analysis and XY plotting of single variable data.

This month we concatenate a series of 2-D slices — horizontal planes from a brain MRI — to generate a 3-D volume.

Below is one solution to this visualization challenge. In reality, several different methods are possible to visualize the MRI data with Tecplot. The article's goal is to demonstrate strategies and tools you can apply to your data.

Step 1: Loading the 2-D MRI Slices
1. Load ( MRI_Data.zip 248 KB ) eleven MRI slices — 17 through 27 (basically the top of the head).
The 2-D slice data consists of I, J and and an intensity variable (INT).
In Tecplot, eleven new zones are created from the MRI slice data.

2. Play the zonenum.mcr macro to create a new Z-axis variable equal to the zone number.
Because our third variable is intensity, the Z-axis information will be temporarily stored as variable 4.

3. On the Data Set Information dialog four variables are visible including new Z-axis variable V4. V4 goes from 1 to 11 — matching the zone number.

4. Open the Specify Equations dialog.

5. Modify the data using the Specify Equations dialog.
a. Make a new variable V5. Move intensity (V3) to the new V5 variable. V5=V3.
b. Move the Z-axis information in V4 to V3 (the standard Z-position). V3=V4.
Click Compute .

6. On the Data Set Information dialog change variable 3's name to K.

7. Switch to 3D frame mode.
The 11 MRI slices are visible.

8. The actual MRI slices are about 3 units apart.
In Tecplot we set the Z-distance equal to the zone number — thus they are 1 unit apart.
Using the Specify Equations dialog, generate a volume that is similar in dimension to the actual object. V3=V3*3.
Click Compute.

9. On the Edit Axis dialog (Axis/Edit), switch the dependency to XYZ dependent.

10. Reset the 3-D axis (Axis/3D Axis Reset) and fit the data (Axis/Fit to Full Size).
The resulting image will look like this.

11. To generate a 3-D volume from the slice data, write the data out.

12. Write out variables of interest: V1, V2, V3 and V5.
Write out field data in ASCII POINT Format. Use a precision of 3.
(V4 is the Z-axis information identical to V3.)
Save the new file as output2d.dat .

13. After writing the data out, preview the current data.
a. Turn off the Mesh and Boundary zone layers. Turn on Contour.
b. Display zone 1.

14. Zone 1 looks like a brain MRI slice.

Ultimately we want to see a 3-D image of the brain MRI slices.
The next step is to concatenate the 2-D slices.

Click here for Step 2.

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