Sean Lauber:AMIRA - Creating Label Fields by Lung Segmentation

In order to evaluate changing densities in the lung of an affected animal, you need to

separate the lung portion of the CT scan from the rest of the CT scan. This is done by

creating a lung "label field". One method of generated a lung label is by a process

called "thoracic segmentation".

The idea is to color in sections of the lungs, using the ribs as a guide, and interpolate

the label between sections. This will generate a 3D segmentation of the lung which can

subsequently be analyzed for density values by histogram analysis.

1. Open the relevant .raw file

2. Adjust the parameters accordingly. For data from the MCPTI I use the following

parameters:

3. Then open the Segmentation Editor (see the cursor):

4. In the Segmentation Editor, open a New Label Data file (see the cursor), and the lung

CT data will load:

5. Add a New Material (see cursor, in this case Material2) so you can add label data to a

material file.

6. I like to adjust the Data Window to better show the CT data

7. Select the Paint tool so you can begin coloring in the lung label. I like to use a

point size of 60 to begin, and as I move on increase the size to 100.

8. Bring up the position of the CT scan towards the head (either scroll up/down over the

CT image or adjust the bar directly below the CT image). Position the image to show the

first set of ribs (see figure) and color in the area (shown in red in the figure, this

should take a single click of the mouse).

9. To clean up the image, hold down ctrl and click the mouse to delete label, use this

feature to exclude the region surrounding the spinal cord.

10. Scroll down approximately 3 ribs (watch the ribs emerge from the spinal cord area),

then color in this lung section. Delete the label surrounding the spinal cord (as shown

in the figure).

11. Next we want to interpolate the label that you made at the first set of ribs to the

label you just made at this 4th set of ribs. To do this go to Selection/Interpolate or

press ctrl-I. Scroll up and down to verify that the interpolation worked.

12. From the 4th set of ribs, go down another 3 sets. Color in this area (I like to use

paint brush size 100 from here on), remove spine label, and interpolate.

13. From this 7th set of ribs, go down until you see the diaphragm begin to appear. This

is located just below the heart. Color in this area, remove spine, and interpolate.

14. From the region of the diaphragm, scroll down until you don't see any lung left.

Color in this region as indicated, remove spine and interpolate. You don't want to color

the whole of this region because much of it is not lung, and you want to color it in in

the indicated shape so when it interpolates upwards it forms the desired shape.

15. The lung segmentation is now complete!

16. To save the label, add the label to the material (Material2) by clicking the + sign

(see cursor). Make sure you have Material2 highlighted, if you have nothing

highlighted, then the label you've just created will be lost.

17. Return back to the Object Pool (the section you were in at the beginning of this

lesson - its the first symbol on the top left, 2 symbols back from the Segmentation

Editor symbol)

18. Right click on the label (now below the .raw file) and save the file. Make sure

to save the file as .RLE