The overall goal of this protocol is to provide a reliable, anatomically accurate method for segmenting the human hippocampus with subfields on magnetic resonance images. Here, the hippocampal subfields are divided into five labels, CA one, CA two, ca three, CA four, dentate gyrus, S-R-S-L-S-M, and the icm. This method can help answer key questions in the neuroimaging field, such as how hippocampal subfield structure changes in healthy and disease states.
The main advantage of this technique is that it is tailored to high resolution images collected on a three T scanner, and it includes subfield definitions for the entire anterior posterior length of the hippocampus. Begin by entering the following command scene here into the terminal. To open the software interface on a T one weighted image, enlarge the coronal view and zoom in on the hippocampus, select segmenting in the navigation window, and then select XY radius.
Set the XY brush size to 0.1. Scroll to the anterior most coronal slice of the hippocampus for slice a, the anterior mott slice. Draw the outermost border of the hippocampal gray matter where it meets the surrounding temporal lobe white matter, and use the high intensity white matter of the alves to assist with the superior border.
Use the label fill key in the segmentation menu of the navigation window to fill in the label inside the border. For slice B, the hippocampal head won. Continue to draw the borders of the hippocampal head by using the white matter of the temporal lobe and alves as a guide.
Next for slice C, the hippocampal head two with dations. Draw the dations of the hippocampus by using the white matter of the alius. Then use the axial view to draw a horizontal line from the anterior edge of the lateral hippocampus and designate anything below this line as part of the hippocampus.
Now for slice D, the hippocampal head, three, draw the inferior border of the hippocampus at the white matter of the temporal lobe and the lateral border at the inferior horn of the lateral ventricle. Draw the superior border at the white matter of the alius fibr and the medial border at the hypo intense region of the ambient cistern. For slice, E, draw the inferior lateral superior, and medial borders.
As before, define the infer medial border by drawing the inferior portion of the medial border where the hippocampus thins slightly and extends into the gray matter of the interal cortex. In these slices, include the onus in the hippocampal segmentations. Then designate the hippocampal body on slice F.As before, do not include the low intensity cerebral spinal fluid of the vestigial hippocampal sulcus in the segmentation.
Now for slice G segment, the hippocampal tail begin segmenting the tail. When the cruise of the fornix is first visible. Exclude the vesicular gyrus by extrapolating the shape of the vesicular gyrus into the hippocampal tail for more anterior slices.
When the vesicular gyrus can no longer be distinguished, treat all visible gray matter as hippocampal tail. Then for slice H, the hippocampal tail two segment, the low intensity gray matter of the posterior hippocampal tail from the surrounding high intensity white matter. Finally, or slice eye, the posterior most slice segment, the small remaining area of the hippocampal gray matter from the surrounding white matter of the temporal lobe.
Begin by scrolling to the anterior most coronal slice of the hippocampus on a T two weighted image. Change the color of the paintbrush by selecting set paint label and entering a number between one and 255 in the terminal. For slice A, the anterior most slice, draw a line dividing the visible hippocampal gray matter along its longest visible axis into two equal sections.
Use two different colors to label the superior of these two sections as ca one and the inferior section as the sulu for slice B, the hippocampal head one. Label the low intensity area in the middle of the hippocampal formation. As SR SLSM, define the inferolateral csum ca one border at the bend in the inferior hippocampus.
Continue to follow the longest axis of the hippocampus to draw the ca one sulu border on the superior medial tip for slice C, the hippocampal head. Two with temptations. Label the dark S-R-S-L-S-M band that follows the curve of the ca one label, any high intensity gray matter inside of the S-R-S-L-S-M as CA four dg.
Then define the sicm ca one border using the bend and the inferior hippocampus. Define the border between CA one and ca two, CA three as a 45 degree angle line, extending in the superolateral direction from the most superolateral edge of the S-R-S-L-S-M. Extend the ca two CA three medially along the superior edge to the trough between the dations and label the rest of the superior edge as ca one for slice D, the hippocampal head three.
Label the S-R-S-L-S-M CA four, DG and ICM exactly as just described. For slice C, extend the CA two, CA three medially halfway along the superior edge, and label the other half of the superior edge as CA one. Divide the super medial hippocampal head vertically in half.
Label the medial half as S-R-S-L-S-M. Then horizontally, divide the lateral half in half. Again, label the inferior portion as CA two, CA three, and label the superior portion as CA four DG for slice E, the hippocampal head four with Angus.
Define the saeculum ca one border as a vertical line extending in the inferior direction from the most medial edge of the CA four dg. Continue to define the CA one, CA two, CA three s, RSL, SM, and ca four DG borders. As before, label the onus of the hippocampus as the hippocampal head transitions into the hippocampal body in the onus label, the low intensity region in the center as the SRSL sm.
Continuing on slice E, draw a line at the superior edge of the S-R-S-L-S-M section along the inferolateral super medial axis of the UCAS label. All gray matter above this line as CA two, CA three, label any unlabeled gray matter below this line as CA four D.Next, or slice F, the hippocampal body. Continue to apply the borders for the sulu S-R-S-L-S-M ca four, DG ca two, CA three as mentioned for slice E on slice G, the hippocampal tail one.
The ICM ca one border becomes a 45 degree angle line, extending in the infra medial direction from the medial edge of the CA four DG for slice H.The hippocampal tail two label the low intensity inner layer as S-R-S-L-S-M and the outer high intensity layer as CA one. Once the vesicular gyrus can no longer be distinguished from the hippocampal formation label any remaining gray matter in the middle as CA four dg. Finally, for slice eye, the posterior most slice leave the entire structure as CA one.
Once the dark S-R-S-L-S-M is no longer visible in the hippocampal formation, this protocol uses magnetic resonance imaging to segment the human hippocampus. Here, the whole hippocampus is divided into nine coronal slices using T one weighted images. Five, hippocampal subfields are then segmented using T two weighted images here, the CA one, CA two, CA three, CA four, denate gyrus, S-R-S-L-S-M and ICM can be seen within this hippocampal head slice.
Once mastered, this technique can be completed for each subject in 40 hours if it is performed properly. It's important to remember to follow intensity patterns in the images as much as possible and be consistent with borders between subjects following this procedure. Other automated segmentation techniques can be performed to answer questions about the volume and shape of the hippocampus in vulnerable populations such as those undergoing healthy aging or suffering from Alzheimer's disease.
After watching this video, you should be able to reliably replicate this protocol and gain insight into the detailed hippocampal subfield anatomy of your subjects.
