Volumetric Analysis of Volumetric Analysis of Brain Structures Using Brain Structures Using

MR ImagingMR ImagingLilach Shay, Shira NehemiaLilach Shay, Shira Nehemia

Bio-Medical EngineeringBio-Medical Engineering

Dr. Alon Friedman Dr. Alon Friedman and Dr. Akiva Feintuchand Dr. Akiva Feintuch

Department of Physiology,Department of Physiology,Faculty of Health Sciences Faculty of Health Sciences

Basic Principles of MRIBasic Principles of MRI

The Human body mainly The Human body mainly consist of waterconsist of water

The concept of MRI is The concept of MRI is based on the fact that based on the fact that hydrogen nuclei have hydrogen nuclei have magnetic properties, magnetic properties, called called nuclear spinnuclear spin

Macroscopic, they behave Macroscopic, they behave like tiny rotating magnets, like tiny rotating magnets, represented by vectorsrepresented by vectors

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Magnetization VectorMagnetization Vector Within a large external magnetic field Within a large external magnetic field

(called B0), nuclear spins align with (called B0), nuclear spins align with the external field. Most of the spins the external field. Most of the spins align with the field (parallel) and some align with the field (parallel) and some align against the field (anti-parallel)align against the field (anti-parallel)

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Larmor FrequencyLarmor Frequency The resonance frequency, called The resonance frequency, called Larmor Larmor

frequencyfrequency ( (ωω00) or precessional frequency, is ) or precessional frequency, is proportional to the main magnetic field proportional to the main magnetic field strengthstrength

Larmor Larmor FrequencyFrequency

Geomagnetic ratio Geomagnetic ratio andandis a constant is a constant unique to every unique to every atom atom (H(H++=42.56 =42.56 MHz/Tesla)MHz/Tesla)

ExternaExternal l magnetmagnetic field ic field

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Basic principles of MRIBasic principles of MRIA A magnetmagnet is a dipole and it can be is a dipole and it can be

represented by a magnetic vectorrepresented by a magnetic vector. . A moving A moving magnetic field induces a current in a coilmagnetic field induces a current in a coil. .

For example, the rotating magnet below For example, the rotating magnet below induces a sinusoidal current that can be induces a sinusoidal current that can be recorded.recorded.

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Volume and AtrophyVolume and Atrophy Quantitative volume measurements of Quantitative volume measurements of

specific brain regions are essential for specific brain regions are essential for research of brain diseases and may research of brain diseases and may prove of diagnostic value (e.g. prove of diagnostic value (e.g. neurodegenerative diseases).neurodegenerative diseases).

Diagnosis

Decision upon treatment

Monitor treatment efficacy

Insight into pathological mechanisms

Hippocampus and Cerebral Hippocampus and Cerebral CortexCortex

Takes part in memory and Takes part in memory and spatial navigation spatial navigation

Consists of a mixture of Consists of a mixture of grey matter and white grey matter and white matter matter

h ttp :/ /w w w .th o m asko e n ig .c h /Le s te r / ib a sp m .h tm

Schmolesky M., 2000

Outermost thin layer of grey matter Outermost thin layer of grey matter in the brain in the brain

Many brain functions: Many brain functions: memorymemory, , attentionattention, perceptual , perceptual awarenessawareness, , languagelanguage and and consciousnessconsciousness

Difficulties of Brain Difficulties of Brain Volume EvaluationVolume Evaluation

Signal intensity of Signal intensity of grey matter and grey matter and white matter vary white matter vary within the brainwithin the brain

Contrast of white Contrast of white - grey matter is - grey matter is relatively dimrelatively dim

Partial volume Partial volume effecteffect

ArtifactsArtifacts

Review of Segmentation Review of Segmentation MethodsMethods

1. Grey level thresholding1. Grey level thresholding

2. “Edges” method2. “Edges” method , ,

- checking neighbor voxels- checking neighbor voxels

3. Statistical method - Bayes 3. Statistical method - Bayes correctioncorrection

4. The manual segmentation4. The manual segmentation

22),( yxyxE kyxE ),(

kg

Bayes Bayes lawlaw

)(

)|()|(

gP

ngPgnP

tot

The probability to The probability to get a specific grey get a specific grey

level valuelevel value

The label The label probabiliprobabili

tyty

The likelihood The likelihood component of the component of the

tissuetissue

Review of segmentation Review of segmentation methodsmethods

)3|()2|()1|()( gPgPgPgPtot

Thacker et al., 2004

Up until nowUp until now Literature reviewLiterature review Review of software Review of software

packages:packages:

1. 1. MRIcroMRIcro - - -converts the data -converts the data from slices of 2-D from slices of 2-D matrixes into one matrixes into one matrix only (3-D) matrix only (3-D)

-the MRI data -the MRI data viewer. viewer.

Review of Software Review of Software PackagesPackages

2. 2. SPMSPM--

(Statistical (Statistical Parametric Parametric Mapping) .a Mapping) .a MATLAB MATLAB software package.software package.

Allows us to Allows us to perform perform spatial spatial normalization normalization and smoothing and smoothing (Bayes (Bayes correction) of the correction) of the data. data.

We have performed 2 MRI scansWe have performed 2 MRI scans Different sequences: Different sequences:

- - T1T1: : Recovery of Recovery of longitudinal longitudinal magnetization magnetization

- - T2T2: Decay of transverse : Decay of transverse magnetization magnetization

- IR (Inversion Recovery) - IR (Inversion Recovery)

- FLAIR (Fast fluid attenuated inversion - FLAIR (Fast fluid attenuated inversion recovery) recovery)

- Grey Matter only- Grey Matter only

Performing Brain MRI Performing Brain MRI ScansScans

Computer Vision Laboratory at UMass,2003

Writing a MATLAB Writing a MATLAB scripts that: scripts that:

1. analyzes SPM-1. analyzes SPM- generated generated outputoutput

2. produces a mask 2. produces a mask of of Grey Matter Grey Matter

3. 3. Segmentation of Segmentation of Grey Grey Matter applied Matter applied on T1-on T1- weighted MRI weighted MRI

Data AnalysesData Analyses

Segmentation Segmentation of of Grey Matter Grey Matter applied on T1- applied on T1- weighted MRI weighted MRI

Up until nowUp until now

Choosing the optimal sequence Choosing the optimal sequence (minimal error) (minimal error) for grey matter segmentation. for grey matter segmentation.

Validating the developed tools by Validating the developed tools by measuring measuring grey matter volume in a sample of grey matter volume in a sample of controls and controls and neurological patients. neurological patients.

Develop mathematical tools for Develop mathematical tools for delineating the delineating the cerebral cortex and the cerebral cortex and the hippocampus from sub-hippocampus from sub- cortical grey matter. cortical grey matter.

Future TasksFuture Tasks

The EndThe EndQuestions ?Questions ?