General Description
Our definition of the hippocampus includes the hippocampal formation and is
comprised of the dentate gyrus, the ammonic subfields (CA1,CA2, CA3, CA4)
, the prosubiculum, and the subiculum. The hippocampus is located in the
medial region of the temporal lobe, bulging in the floor of the inferior
horn of the lateral ventricle. Anteriorly, and to some extent superiorly,
it borders with the amygdaloid nuclear complex (amygdala). Laterally, the
hippocampus borders with the temporal horn of the lateral ventricle. The
medial border of the hippocampus is mainly with subarachnoid cerebro-spinal
fluid (CSF). Inferiorly, the border between the hippocampus and entorhinal
cortex (PHa) as well as posterior parahippocampal gyrus (PHp) is demarcated
by white matter. The caudal end of the hippocampus is situated under the
pulvinar, medial to the trigon of the lateral ventricle, whereas the rest
of it is surrounded by white matter, and medially by subarachnoid CSF.
Segmentation Procedure
The
hippocampus is segmented using a contour line and manual editing. In its
anterior extent, the hippocampus is very difficult to distinguish from the
amygdala. Sulci lines drawn in the sagittal views to separate the amygdala
and hippocampus are necessary to segment the hippocampus.
Part I - Sulci lines
Draw sulci lines in the sagittal view to separate the hippocampus from the
amygdala. Start with one side of the brain and move to approximately the
most lateral extent of the amygdala. On this slice you will see the hippocampus,
a large portion of the inferior lateral ventricle (ILV), and a small gray
area that is the amygdala.
Continue
to scroll the sagittal image medially. As you do, the size of the IL V will
decrease, and the grayness of the amygdala will become more pronounced. When
the ILV is very thin, and the amygdala and hippocampus look as if they will
touch soon, draw a sulci line from the superior to the inferior border of the
IL V, right in the middle of the ventricle, separating the hippocampus from
the amygdala.
Continue
to move medially, and continue to draw sulci lines bisecting the ILV. Draw
sulci lines only on slices where you can see the border between the hippocampus
and the amygdala.
Part II - hippocampus and amygdala coexist
When the temporal horn of the lateral ventricle is first visible, it is likely
that the hippocampus is present. Use your sulci lines to guide the hippocampal
borders.
To segment the hippocampus in this area, use a contour line to define the hippocampus-amygdala
area by using your sulci lines. Depending on the brain, you will see darker
pixels that represent the ILV, or brighter pixels that represent the fimbria
of the hippocampus (or both) along your sulci lines. If possible, draw a line
separating the amygdala from the hippocampus along the dark pixels of ILV.
Try increasing the contrast between black and white to better see this division.
If after manipulating the brightness/contrast this line is not visible, draw
a line that bisects your sulci lines. Then use projection lines to verify that
the line really is the division between the hippocampus and the amygdala. When
you are satisfied, unextract the hippocampus-amygdala (hipp-amyg) outline,
and extract the bottom portion as hippocampus.
At this level, the hippocampus will appear as a small sliver, most likely along the medial border of the hipp-amyg area. To accurately define the medial border of the hippocampus, change the intensity of the screen to brighten the white matter pathway that separates the hippocampus from the cortex. Continue to segment the hippocampus in this manner as you move posteriorly. First use a contour line to define the hipp-amyg area, then edit the borders as necessary (i.e. along the medial border). Use your sulci lines as a guide for the separation between the amygdala and hippocampus. Draw in this border. Unextract the hipp-amyg outline, and re-extract the hippocampus separately. As you move posterior the division between these two takes on a saw-tooth pattern.
Also, the hippocampal area will increase as the amygdala area decreases.
A common error in segmenting the hippocampus is to include partial voluming of the IL V and white matter in your outline. The hippocampus does not extend laterally past the IL V. If part of your outline for the hippocampus does, edit as necessary.
Part III - amygdala disappears
When the amygdala is no longer present, a contour line is needed to outline
the hippocampus. Depending on the brain, the inferior and superior borders
of the hippocampus may not be adequately captured using one contour line.
If this is the case, cut and paste multiple contours using the "v" function
as described previously. At this 
point,
the fimbria appear as thin white stripes at the dorsal edge of the hippocampus.
You may find that the fimbria are being excluded from the hippocampus when
you use the intensity contour function. If necessary, manually draw in the
superior border of the hippocampus above the fimbria.
A common error in this area of the hippocampus is to include partial voluming of the IL V in the hippocampus outline. Make sure the hippocampus does not extend lateral or superior to the ILv.
The inferior medial border of the hippocampus, which will include the subiculum, most of the presubiculum, and about a quarter of the parasubiculum, follows the trajectory of the white matter within the parahippocampal gyrus.
Part
IV – hippocampus and thalamas coexist
As you continue to move posterior, the hippocampus will start to share a border
with the thalamus. To determine what is thalamus and what is hippocampus, projection
lines are needed. At about this area, the fimbria are no longer visible, and
therefore no white matter strip is included in the hippocampus outline. Using
the sagittal view is helpful in distinguishing this transition.
Part
V- thalamas disappears
In its posterior extent, the hippocampus will border the lateral ventricle,
and will become large after the thalamus is not present anymore. In its most
posterior extent, the hippocampus will border the lateral ventricle laterally,
and white matter medially.
Extraction
As with all sub-cortical structures, first extract the hippocampus from the
outside. Hit "x" to get rid of stray contours. Then extract the
hippocampus from the inside.
Labeling
The hippocampus is labeled as "hippocampus".
© 2005 Neuromorphometrics, Inc. All rights reserved.