VOI colored display on anatomical

This page describes how to create an image with VOI colored according to a specification, as below.

This image was created using mricron and SPM. The approach is as follows:

1. Create a combined VOI file with each VOI represented by a different number (1, 2, 3, ...).
   • You can do this manually using imcalc; select two VOI files, and enter an expression i1+i2*2+i3+3 to set image values for three VOI to be 1,2 and 3.
   • Alternatively in CSPM: in the Display Results GUI, after you have loaded the VOI, select the VOI you want to combine, and click the "Show colors" button on the bottom right.
2. Create a "look-up table" (LUT) file that assigns a color to each number; colors are RGB values.
   • Example: insula.lut 
   • In CSPM: a LUT is created when you click "Show colors", based on the timetrends you have selected.
   • This is a text file, with a value corresponding to an RGB color. In the insulat.lut example, we only have 10 VOI's, so most of the values are set to 0 (the lut must have 256 entries).
3. Copy this LUT file into mricron's LUT folder
   • Typically C:\Program Files (x86)\mricron\lut
   • Next time you open mricron, you will see the name of this LUT as an option ("2" in example on right).
4. Open an anatomical, and overlay the combined VOI file.
5. Select the LUT from mricron's menu, and set the display range to be 0.01 - 255. (The 0.01 value is a very small number close to zero; other small values would work.)

Insula example