Electronic Thesis and Dissertation Repository

Thesis Format

Integrated Article


Master of Science




Khan, Ali R.

2nd Supervisor

Duerden, Emma G.


The human amygdala is composed of 13 functionally and anatomically distinct subnuclei. Because most nuclei are difficult to distinguish at the microanatomical level, they are also challenging to discern macroscopically. In low field strength magnetic resonance imaging (MRI) studies, the amygdala can be identified only in its entirety. Higher resolution scans can be acquired by employing ultra-high field strength MRI acquisition techniques. We present a step-by-step guide for the manual segmentation of the amygdala subnuclei at ultra-high field 9.4T MRI. Post-mortem human brain specimen amygdala prosections fit for the 9.4T MRI bore allowed for the collection of high resolution T2-weighted images and visualization of all subnuclei. Intra and inter-rater reliability results suggest this yields a precise protocol leading to greater amygdala subnuclei labelling accuracy applicable for future research investigating substructure functions. The aforementioned ex-vivo neuroimaging methodologies can be implemented in the investigation of other subcortical brain structures.

Summary for Lay Audience

The amygdala is a tiny almond shaped structure located deep within the brain. The amygdala’s substructures are especially important due to their implications in anxiety and neurological disorders like Alzheimer’s disease. Only through the use of post-mortem specimen data acquisition at ultra-high magnetic field strength MRI (magnetic resonance imaging) can we delineate the human amygdala subnuclei. MRI is a tool which uses magnetic fields and radio waves instead of x-rays to generate images of the organs within the body. When one suffers from a chronic migraine or a suspected concussion, a doctor may order an MRI scan to take a close look inside the head at the brain. MRI makes use of the water molecules throughout your body. While MRI machines are predominantly used in diagnostic medicine in patients, they can also be used to form images of post-mortem specimens. There are many types of MRI scanners, some are more powerful because the magnet is stronger. With a stronger MRI machine, resulting images may provide higher quality pictures of the brain. The more powerful the scanner, the better the result. Scanning post-mortem human brain specimens at strong MRI scanners for long periods of time without detriments like motion leads to high contrast between the grey and white matter of the brain tissue. This contrast allows for the visualization of the even smaller internal parts of the amygdala, deep within the brain.

The amygdala is imaged in its entirety at lower strength MRI but the examination of its internal details requires the improved resolution provided by ultra-high field MRI scanners. By manually contouring 13 distinct amygdala grey matter substructures individually on MRI images allowed for the development of a highly reproducible manual segmentation protocol. Segmentation of the amygdala substructures on MRI scans provided measurements of their volumes and will provide better clues of underlying in vivo anatomy and pathologies. If the substructures are anatomically mapped out with structural MRI, individual functions can become better understood. They may be specifically relevant to certain etiologies.

Available for download on Friday, March 31, 2023