Integrated Studies
Applied Neuroscience Seminar
Evan Fletcher, Mario Ortega
Dr. Charles DeCarli, IDeA Lab Director
Overview of Course
- OVERVIEW
- Introductory Lecture
- Lab Hours involving computer based image analysis (Mario,
Evan)
- LECTURE
-
Introductory Lecture (today) including:
Basics of Neuroanatomy, Software Overview of Laboratory
MRI Imaging Basics
Memory Decline with Aging
- LABORATORY
- Longitudinal Hippocampus Project
- Testing a possibility programs under development
- Trace a hippocampus at initial time and apply it to future scan
using computer modeling and “warping”
Studies of Brain Form and Function
• Postmortem brains (not us!)
Used for precise anatomical
measurements
• Living subjects (computer analysis)
Use MRI imaging to track form and
function in living individuals
Basics of Brain Anatomy
• Next slides show postmortem images to
illustrate large anatomical features
• Good for precise anatomical
measurements
• Cannot study changes during life
(obviously!). For that, need MRI
The Human Brain
Cerebrum
-Divided into four regions, Frontal, Parietal. Occipital, Temporal
-Highly convoluted surface with 6 layers of cells in the cortex.
Meninges
-the brain has several layers of protection, internal to the skull, these are the meninges.
-On an MRI image the different layers are not discernable.
-They provide protection, drain the Cerebrospinal Fluid, and blood input and output.
Four Cerebral Lobes
(viewed from midline)
MRI Images
• Magnetic Resonance Imaging
• Intense magnetic and radio frequency
fields
• Quantum mechanics
• Pinpoint small features in living brain
• Lauterbur and Mansfield – Nobel Prize
2003
Sample MRI Images
• High resolution
anatomical MRI
• 3D and 2D views
• Skull in place and
stripped
These images were viewed using “Slice Viewer” a program you will
see in this lab.
We will show you images so you can learn the basic structures and
how to separate brain from meninges.
Anatomical Basics from MRI
• The next slides show brain features
relevant to longitudinal studies of living
individuals
• Longitudinal studies
-Track changes in form and function for
same individual over time
More Anatomical Basics
Young and Old
• These images show
comparable slices of
young and old brain
images.
• Compare features for
changes:
– Ventricles
– Hippocampi
– Sulci
Our focus: Hippocampus
Next slides will explore the hippocampus
which is the focus of your research project
Points about the hippocampus:
1. Seat of long-term memory formation
2. Subject to early deterioration in
Alzheimer’s Disease
The Hippocampus
Hippocampi and Ventricles
Hippocampus
(purple)
An elephant never forgets
• This shows the huge
and convoluted
hippocampus of an
elephant (red)
• Greater hippocampus
volume to brain ratio
than in humans
Our Research Project:
Longitudinal Hippocampal Change
• Hippocampus is a main site of
degeneration in dementia
• Acquire brain image at time 1 and time 2
• Trace (manually) hippocampus at time 1
• “Warp” time 1 onto time 2
• Use the warp to automatically compute
hippocampal volume at time 2
Warping
• No two brain images are alike
• Even for time 1 and time 2, local changes
will occur
• Warping is a technique for computing
these changes and morphing one image
onto another
• It can highlight brain changes and
compute differences
Uses of warping
• Slides show two
views of longitudinal
change
• Left panels: earlier
time
• Middle: later time
• Right: color-coded
views of shifts
• Changes computed
by warps
Your Role in Research
•
•
Overall goal: track hippocampal volume
changes in 20 subjects
Steps
–
–
–
–
–
Strip skulls from images
Align time 1 and time 2 brains
Trace hippocampus in each time
Warp time 1 to time 2
Compute hippocampal volume changes
Things you will learn
1. Navigation in linux computers:
Basic linux commands
2. Using software tools in linux environment
3. Basic brain anatomy focusing on
hippocampus (Mario)
4. Tracing techniques (Mario)
5. Concepts of image warping and
volumetric calculations