Measurement of the Entorhinal Cortex 1. Open ITK

Measurement of the Entorhinal Cortex
1. Open ITK-Snap
2. Open the “Finder” window and locate the file for the brain you want to work on
3. Drag and drop this file into the ITK-Snap window
4. Look at the sagittal view and check to make sure the scan is AC-PC aligned
5. Proceed to the coronal view. Starting at the front of the brain, move posterior
until the limen insulae can be seen. Record the slice number at this location. In this
example, slice # 127/218.
6. Scroll two slices posterior to begin measurement of the entorhinal cortex. Record
the slice number at this location. Ex. #125/218.
7. The medial border is of the entorhinal is the suclus semiannularis. The lateral
border depends on the depth of the collateral suclus.
a. Shallow (<1 cm): Measure to the fundus of the collateral suclus (inner
b. Regular (1 to 1.5 cm): Lateral border is the midpoint of the medial bank of
the collateral sulcus
c. Deep ( > 1.5 cm): Lateral border is the medial edge of the collateral sulcus
To determine the depth of the collateral sulcus, open Osirix and selec the brain you
are looking at.
A window should appear with the scan and a toolbar will be displayed at the top of
the screen. The magnify tool will enlarge or shrink the scan.
Locate where the limen insulae is formed and find the collateral sulcus.
The length tool can be used to measure the depth of the sulcus.
Be sure to check the depth throughout the entorhinal cortex to account for any
Using, the polygon tool, outline the entorhinal cotex.
To fill in the polygon, right click inside the I figure and select “close loop & accept”.
The paint brush tool can be used to touch up any errors.
8. The most caudal slice should be 2 slices after the end of the uncus (use the
beginning of the pons for reference. Ex. #114/218.
9. To view the measured entorhinal in 3D, go to the blank window and click “update
You can zoom in on this view by clicking the rotate tool in the 3D Toolbox, right
clicking on the 3D mesh and moving the mouse up to zoom in and down to zoom
You can also pick a specific spot by clicking the crosshairs tool in the 3D Toolbox
and clicking on a spot on the mask. This will pinpoint the spot in each window.
This tool can be useful for cleaning up any odd parts on the 3D mesh.
10. To save your image, click on “Segmentation” and “Save as Image”.
A window will pop-up asking for the filename. You can browse and choose a place to
save it or type in a location. Entorhinals should be saved as