1. Volumetric Analysis of Brain Structures Using MR Imaging Lilach Shay, Shira Nehemia Bio-Medical Engineering Dr. Alon Friedman and Dr. Akiva Feintuch Department of Physiology, Faculty of Health Sciences

2. Basic Principles of MRI The Human body mainly consist of water The Human body mainly consist of water The concept of MRI is based on the fact that hydrogen nuclei have magnetic properties, called nuclear spin The concept of MRI is based on the fact that hydrogen nuclei have magnetic properties, called nuclear spin Macroscopic, they behave like tiny rotating magnets, represented by vectors Macroscopic, they behave like tiny rotating magnets, represented by vectors www.e-mri.org

3. Magnetization Vector Within a large external magnetic field (called B0), nuclear spins align with the external field. Most of the spins align with the field (parallel) and some align against the field (anti-parallel) Within a large external magnetic field (called B0), nuclear spins align with the external field. Most of the spins align with the field (parallel) and some align against the field (anti-parallel) www.e-mri.org www.simplyphysics.com

4. Larmor Frequency The resonance frequency, called Larmor frequency (ω 0 ) or precessional frequency, is proportional to the main magnetic field strength The resonance frequency, called Larmor frequency (ω 0 ) or precessional frequency, is proportional to the main magnetic field strength Larmor Frequency Geomagnetic ratio and is a constant unique to every atom (H+=42.56 MHz/Tesla) External magnetic field www.e-mri.org

5. Basic principles of MRI A magnet is a dipole and it can be represented by a magnetic vector. A moving magnetic field induces a current in a coil. For example, the rotating magnet below induces a sinusoidal current that can be recorded. www.e-mri.org

6. Volume and Atrophy Quantitative volume measurements of specific brain regions are essential for research of brain diseases and may prove of diagnostic value (e.g. neurodegenerative diseases). Quantitative volume measurements of specific brain regions are essential for research of brain diseases and may prove of diagnostic value (e.g. neurodegenerative diseases). Diagnosis Decision upon treatment Monitor treatment efficacy Insight into pathological mechanisms

7. Hippocampus and Cerebral Cortex  Takes part in memory and spatial navigation  Consists of a mixture of grey matter and white matter http://www.thomaskoenig.ch/Lester/ibaspm.htm Schmolesky M., 2000  Outermost thin layer of grey matter in the brain  Many brain functions: memory, attention, perceptual awareness, language and consciousness

8. Difficulties of Brain Volume Evaluation Signal intensity of grey matter and white matter vary within the brain Signal intensity of grey matter and white matter vary within the brain Contrast of white - grey matter is relatively dim Contrast of white - grey matter is relatively dim Partial volume effect Partial volume effect Artifacts Artifacts

9. Review of Segmentation Methods 1. Grey level thresholding 2. “ Edges ” method, - checking neighbor voxels - checking neighbor voxels 3. Statistical method - Bayes correction 4. The manual segmentation

10. Bayes law The probability to get a specific grey level value The label probability The likelihood component of the tissue Review of segmentation methods Thacker et al., 2004

11. Up until now Literature review Literature review Review of software packages: Review of software packages: 1. MRIcro - -converts the data from slices of 2-D matrixes into one matrix only (3-D) -the MRI data viewer. -the MRI data viewer.

12. Review of Software Packages 2. SPM- (Statistical Parametric Mapping).a MATLAB software package. (Statistical Parametric Mapping).a MATLAB software package. Allows us to perform spatial normalization and smoothing (Bayes correction) of the data. Allows us to perform spatial normalization and smoothing (Bayes correction) of the data.

13. We have performed 2 MRI scans We have performed 2 MRI scans Different sequences: Different sequences: - T1: Recovery of longitudinal magnetization - T1: Recovery of longitudinal magnetization - T2: Decay of transverse magnetization - T2: Decay of transverse magnetization - IR (Inversion Recovery) - IR (Inversion Recovery) - FLAIR (Fast fluid attenuated inversion recovery) - FLAIR (Fast fluid attenuated inversion recovery) - Grey Matter only - Grey Matter only Performing Brain MRI Scans Computer Vision Laboratory at UMass,2003

14. Writing a MATLAB scripts that: Writing a MATLAB scripts that: 1. analyzes SPM- generated output 2. produces a mask of Grey Matter 3. Segmentation of Grey Matter applied on T1- weighted MRI Data Analyses

15. Segmentation of Grey Matter applied on T1- weighted MRI Segmentation of Grey Matter applied on T1- weighted MRI Up until now

16.  Choosing the optimal sequence (minimal error) for grey matter segmentation.  Validating the developed tools by measuring grey matter volume in a sample of controls and neurological patients.  Develop mathematical tools for delineating the cerebral cortex and the hippocampus from sub- cortical grey matter. Future Tasks

17. The End Questions ?