Part I - anterior portion of third ventricle

1. The third ventricle begins behind the lamina terminalis. In the most anterior slice, the third ventricle is nestled within the optic chiasm. Because the optic chiasm is outside of the brain, the third ventricle appears as a teardrop hanging from the middle of the brain.
2. Use the intensity contour function (press C) to create a contour for the third ventricle. Adjust the contour until it fits tightly around the third ventricle and doesn’t include any gray matter in the outline.

3.  On the second or third slices of third ventricle, use the histogram function to generate the third ventricle outline. Draw a box that contains equal amounts of the CSF from the third ventricle (black), and gray matter  from the thalamus/VDC. 
4. Extract the ventricle outline from the outside (press e)
5. Then unextract from the outside and re-extract from the inside (press i)

Part II-middle portion of third ventricle and beginning of transverse cerebral fissure

1. As the third ventricle continues posteriorly, choroid plexus serves as its dorsal border. This becomes particularly significant at the level of the foramen of Monroe. At times your third ventricle histogram will include the foramen of Monroe and part of the lateral ventricles in your outline.
2. Manually edit your outline using the draw tool so the foramen of Monroe is not part of the third ventricle.

3. Immediately posterior to this level, the TCF begins and continues posteriorly. Draw a circle that is half-way in the ventricle (black) and half-way in the surrounding tissue (gray). Extract the ventricle (press e). Create a historgram (press f).
4. There should be a small contour superior to the third ventricle that represents the TCF. When this small outline appears, begin extracting the TCF also. Create a histogram to extract the TCF. Include equal amounts of CSF from the TCF and gray thalamic tissue in your circle. Use the middle mouse button and move from the highest peak to the next highest peak to get the midpeak for the histogram. Then extract the TCF (press e)

5. Slices at the anterior level of the TCF contain the interthalamic adhesion, which appears to divide the TCF from the third ventricle. Brighten the intensity of the screen. It may be possible to see the choroid plexus that separates these two structures within this "TCF" outline. If it is, manually draw a line just under the choroid plexus.
6. Use a single histogram for the third ventricle and the TCF and then divide the two structures manually. Brighten the screen enough to see the choroid and manually draw a line under it such that the third ventricle and TCF are separated, and extract each independently.

1. At its posterior-most end, the third ventricle becomes almost completely surrounded by TCF. Use the intensity contour function to isolate this small region.
2. Manual editing is often necessary to complete an enclosed area for extraction. Extract the third ventricle first. Then generate an outline for the TCF by creating a histogram between the CSF of the TCF and the thalamic gray matter.
3. As you move posteriorly, the contour you generate will embody both the TCF and the pineal gland. This is desirable because you do not want to include the pineal gland as brain. The third ventricle will appear as a "free-floating" structure inside the TCF outline. Extract the third ventricle then extract the final TCF outline by drawing a line that connects the third ventricle to the TCF. This is done to exclude the third ventricle from the TCF volume.