KTH - Royal Institute of Technology

Visualization

Cerebral Aneurysm and Heart Electrical Signal

Propagation.

Nizar Gandy Assaf Layousse-mail: ngal@kth.se

Javier Lopez Albercae-mail: javierla@kth.se

09/05/2012

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Index

1. Introduction 4

2. Data Description 5

3. Cerebral Aneurysm 63.1. Background . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63.2. Motivation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73.3. Purpose . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73.4. Data Visualization - The Cerebral Aneurysm . . . . . . . . . . . 7

3.4.1. Velocity . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93.4.2. Blood Flow Direction . . . . . . . . . . . . . . . . . . . . 113.4.3. Blood Pressure . . . . . . . . . . . . . . . . . . . . . . . . 113.4.4. Vorticity . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123.4.5. WSS-Wall Shear Stress . . . . . . . . . . . . . . . . . . . 123.4.6. Qvar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133.4.7. Patient Treatment . . . . . . . . . . . . . . . . . . . . . . 14

4. Heart Electrical Signal Propagation 164.1. Background . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164.2. Motivation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164.3. Purpose . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 174.4. Data Visualization - Heart Electrical Signal Visualization . . . . 17

4.4.1. Cardiac Conduction System . . . . . . . . . . . . . . . . . 174.4.2. Heart Beat . . . . . . . . . . . . . . . . . . . . . . . . . . 18

5. Contacts with Pompeu Fabra University and the Evaluation 195.1. @neurIST . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195.2. The evaluation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

6. Tools 20

7. References 21

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1. Introduction

Our project focuses on the study and understanding of cerebral aneurysm,studying its structure and its effect on blood pressure, velocity and the Qvaresteroide (an esteroide that prevents inflammation). An aneurysm is a localized,blood-filled balloon-like bulge in the wall of a blood vessel. Aneurysms cancommonly occur in arteries at the base of the brain and an aortic aneurysmoccurs in the main artery carrying blood from the left ventricle of the heart.It is of interest to mention that previously we have worked on two different dataset, one concerning a study about fuel consumption on different types of carsand the effect of horsepower, weight and displacement among other attributes.The other data set was a result of studying the effect of cpu cycle , cache andmain memory and other atributes on the cpu performance. Both datas lacked ofany geometrical significance thus difficulting the correct visualization of themin 3D dimension a facet that resulted in changing the data set.

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2. Data Description

The whole data set is in CSV format and was a set of points in the space, Usingthe calculator filter we’re able to obtain the vectors corresponding to each threecomponent vectors of velocity, vorticity and Wall Shear Stress (WSS).

The data set describes the flow dynamics of the blood near , through andafter an aneurysim .It was generated by Pompeu Fabra University in Barcelona and its principalattributes (the ones that we will study):

WSS - Wall Shear Stress (dyn/cm2)

Velocity (m/s)

Blood Pressure (mmHg)

Qvar (mcg) : This esteroide is used to reduce inflammation .

Vorticity.

Patient Treatment.

There are 66131 points with roughly 16 attributes .

As for the Heart Electrical Signal Propagation data set the main attributesare:

Heartbeat movement through time.

LAT: Heart propagation electrical signal through time.

Region : Variable to differentiate the left ventricle from the right.

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These data shows the electrical activity in the cardiac conduction system andit’s dimensionality is of 36598 points and 2 attributes (without considering thegeometrical ones).

3. Cerebral Aneurysm

3.1. Background

Many investigation has been done in the past 20 years in this field. In factsome of the papers that we took as reference are from 2005.The potential risk that lies in an aneurysm is the rupture of the bulge that couldcause a wide range of symptoms starting from strong headaches end in partialparalisis of the face and the body.Dr. Iordanis Chatziprodromou and Prof. Dimos Poulikakos from the ETH Zu-rich conveyed a more extensive research that included not only studying theHaemodynamic (blood dynamics) but also were able to simulate and to makepredictions for certain treatments. The complete title of the study is “A Compu-tational Study on Cerebral Aneurysms: Pathogenesis, Aneurysmal Growth andPatient Specific Haemodynamic Simulations”. Some of it’s images :

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But, what is a cerebral aneurysm? which are the symptoms and its charac-teristics? The human brain is supplied by four major blood vessels which areimportant in ensuring a steady supply of oxygen and nutrients to the brain cells.Occasionally, the walls of these blood vessels, supplying to the brain tissue tendto get weakened and result in ballooning or bulging of the blood vessel. Thiscondition is referred to as cerebral aneurysm. Estimates suggest that most indi-viduals with the condition are asymptomatic and it is occasionally an incidentalfinding observed during autopsy.

3.2. Motivation

Given that we’re going to studythe blood flow dynamics inside andaround the aneurysm, we’ve empha-sized the use of stream lines (repre-senting the blood flow) as we considerit’s the most representative algorithmwe can apply to highlight the attri-butes under inspection. In fact , it’sthe main filter/algorithm where theothers in the pipelines are based on tovisualize other aspects like the quan-tity of the Qvar esteroide .

3.3. Purpose

The main purpose of this visua-lization process is to have a betterand thorough insight on the Cere-bral Aneurysm and the implied effecton the blood flow dynamics, pressu-re, wall shear stress force (WSS), andQvar esteroide quantity near the inflammation. Particularly , we’re going tofocus on the blood pressure and analyze how the blood flow behaves insidethe aneurysm , before and after. One of the main questions is the effect of theaneurysm as a blood vessel blocker.As a result of understanding these factors and their effect it would make easierto understand the risk of aneurysm and to apply the adequate treatment. Mo-reover visualizing the treatment data also would give insight and understandingof the healing process (request from the institution in process).

3.4. Data Visualization - The Cerebral Aneurysm

To visualize the data sets , we have used Paraview as the visualization toolfocusing on the relation between the attributes and the geometric meaning (lo-cation of the aneurysm).In this section we are going to explain the various filters and visualization al-gorithms we have applied to obtain a meaningful picture to infer correctly thedesired conclusions. The general visualization pipeline is described by :

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Of which the first stage of the visualization pipeline namely “Data Aqcui-sition” was done by GIMIAS , Graphical Interface for Medical Image Analysisand Simulation of the University of Pompeu Fabra.For better understanding of the data we’ve applied in all specific pipelines forimage creation two algorithms:

Stream Lines Filter: Filter to obtain the flow of blood through thevessels.

Tube Filter: Used to have a better representation of blood flow and givesthe possibility to describe some of the attributes using thickness.

To avoid redundancy , we will ommit them in the following algorithms descrip-tions.

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3.4.1. Velocity

We have coloured the stream lines to get a clear intuition of the flow velo-city. As it’s observable, the blood velocity in the bulge is much lower than itssorroundings confirming the effect of the inflammation on the blood velocityand flow (it weakens and reduces the velocity).

We can apply the clip filter to visualize the velocity of the blood inside theaneurysm.

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3.4.2. Blood Flow Direction

Here we have applied the glyph filter in addition to the basic filters to obtaininformation on the blood flow direction before, through and after the cerebralaneurysm.

3.4.3. Blood Pressure

An important aspect for understanding the effects of the inflammation is theblood pressure.It is observable that the blood pressure before the inflammation is higher thanafterwards, forming a bottleneck and making the flow to lose it’s pressure.

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3.4.4. Vorticity

As part of the blood dynamics study , we were also able to visualize thevorticity of the flow using the filter Warp By Vector thus warping the flowwith the Vorticity vector. Generally as we may expect , vorticity may occur inpresence of velociy and tight curves and we can see in the aneurysm the vorticityeffect is very low due to the low velocity while in some bifurcations it’s higher.

3.4.5. WSS-Wall Shear Stress

WSS is the Wall Shear Stress which is a force applied by the blood flow inthe vessel against the wall. We’ll see from the visualization that generally whenreaching a bifurcation the WSS is bigger as the flow is splitted. The direction ofthe shear stress vector is determined by the direction of the blood flow velocityvector very close to the vessel wall.Here we can see for example that the WSS in the bifurcations is clearly higherthan where there is no bifurcation .

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3.4.6. Qvar

The Qvar is an esteroide that reduces the inflammation (or prevents thesustances that causes the inflammation). Here we visualize the concentration ofthe Qvar esteroide along the vessels .

By visualizing both the Qvar and WSS we could come up with a new evidenceand is that generally where there are high WSS there is more concentration ofthis esteroide.

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3.4.7. Patient Treatment

We’ve managed to obtain from the home institution images for a treatmentof an Aneurysm . The patient , a female with 47 years old diagnosed with anAneurysm in the right Ophthalmic Segment Carotid (right part of the brain wesuppose) .

Both images show the size and the amount of inflammation right starting thetreatment . For the first one we’ve visualized it as a volume but then realizedthat we should apply a slice filter to see the aneurysm . The second image isthe slice of the volume exactly in the middle .

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And both images after six months of treatment and again applied the same filter(slice).

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4. Heart Electrical Signal Propagation

4.1. Background

Heart electrical signal propagation and the heart beat have been studiedextensively in the past. Various simulators like HeartVue give the possibility tovisualize generally the heart and specifically the eletrical signals from variousperspectives.The normal intrinsic electrical conduction of the heart allows electrical propaga-tion to be transmitted from the Sinoatrial Node through both atria and forwardto the Atrioventricular Node.Normal/baseline physiology allows further propa-gation from the AV node to the ventricle or Purkinje Fibers and respectivebundle branches and subdivisions/fascicles. Both the SA and AV nodes sti-mulate the Myocardium. Time ordered stimulation of the myocardium allowsefficient contraction of all four chambers of the heart, thereby allowing selectiveblood perfusion through both the lungs and systemic circulation.Although not a 3D visualization but rather 2D, the ECG (Electrocardiography)is another way to obtain and visualize the electrical signal in the heart. As amere example this could be it’s output.

Unfortunately in our data we don’t have the amplitude of the signal butrather its propagation through time.

4.2. Motivation

In this part we make the visualization of the heart electrigal signal throughtime using mainly color to emphasize the signal propagation. In a healthy heartelectrical signals that originate in specialised muscle cells are propagated th-rough the myocardium and control its rhythmic contractions. When this processis disturbed, an artificial pacemaker may have to be implanted to regularize theheartbeat. Otherwise the resulting arrhythmias can lead to cardiac insufficiencyand sudden death. It has long been known that heritable factors play a part inregulating the electrical activity of the heart. For example, genetic variationscan alter aspects of signal propagation from the physiological pacemaker. In alately large-scale study has identified 22 novel genes that affect impulse conduc-tion in the heart.

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4.3. Purpose

The purpose of this section is to understand the signal propagation insidethe heart, its origin and direction of propagation. A better understanding of theheart electrical signal propagation may lead us to make some useful conclusions.

4.4. Data Visualization - Heart Electrical Signal Visuali-zation

In this case, as in the previous one, the first stage of the visualization pi-peline namely ”Data Aqcuisition”was done by GIMIAS, Graphical Interface forMedical Image Analysis and Simulation of the University of Pompeu Fabra.

4.4.1. Cardiac Conduction System

In this image we only visualize the cardiac conduction system to emphasizewhere the signal is created and how is propagated.

To have an orientation with respect to the heart, we also visualize the heartwith the cardiac conduction system.

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4.4.2. Heart Beat

We saw in the image before where the electrical signal originates and howit propagates. When it reaches to the bottom part of the cardiac conductionsystem it stimulate the heart muscle called the myocardium therefore generatingthe heart beat from bottom to up. Here we have the heart beat through timepropagation.

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5. Contacts with Pompeu Fabra University andthe Evaluation

The need of understanding the data sets and of getting more informationabout the problems that we are trying to visualize made us to contact withPompeu Fabra University. This contact gave us the possibility of learning andunderstanding more deeply about these medical issues. They provided us of acomplete description of the data and information about the aneurist project.As soon as we finish the present report, we will send it to our contact in thisuniversity.

5.1. @neurIST

@neurIST- Integrated Biomedical Informatics for the Management of Ce-rebral Aneurysms - is a European initiative within the Sixth Framework Pro-gramme Priority 2 of the Information Society Technologies IST. This projectis focused on cerebral aneurysms and provides an integrated decision supportsystem to assess the risk of aneurysm rupture in patients and to optimize theirtreatments.

5.2. The evaluation

The evaluation that it has been done is a very simple one. It consisted ofshowing our report to not specialized people and seeing if they understand theproblems, the main properties and conclusions of our visualization graphics. Theresult of this was a complete success since everyone understood perfectly theillnesses with only seeing the graphics.

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6. Tools

ParaView: is an open source, freely available program for parallel, interac-tive, scientific visualization.

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7. References

Graphical Interface for Medical Image Analysis and Simulation , PompeuFabra University .

High fluid shear stress and spatial shear stress gradients affect endothelialproliferation, survival, and alignment by Dolan JM, Meng H, Singh S,Paluch R, Kolega J.

Vascular Wall Shear Stress: Basic Principles and Methods by THEODO-ROS G. PAPAIOANNOU, CHRISTODOULOS STEFANADIS.

@neurIST- Integrated Biomedical Informatics for the Management of Ce-rebral Aneurysms. http://www.aneurist.org

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