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VERTEBRAL CT IMAGES

NAME OF CANDIDATE

Mr. Gundavade Vikas Bhausaheb

NAME OF SUPERVISOR

Dr. Patil S.A.

ABSTRACT

With the growing research on image segmentation of spinal vertebrae, it has become important to

categorise the research outcomes and provide an overview of the existing segmentation

techniques in it. In this project, different image segmentation techniques applied on 3D

segmentation of spinal vertebrae are reviewed. The selection includes sources from image

processing journals, conferences, books, IEEE transactions. The detail survey includes different

approach on segmentation. The state of art research on each category is provided with emphasis

on developed technologies and image properties used by them. The categories defined are not

always mutually independent. Hence, their interrelationships are also stated. Finally, conclusions

are drawn summarizing commonly used techniques and their complexities in application.

1. INTRODUCTION

Accurate vertebra segmentation in computed tomography (CT) images is important for numerous

medical applications, e.g., diagnosis of osteolytic or osteoblastic cancer metastases within the

spinal column [41], diagnosis of spine trauma, and detection of osteoporosis [32]. Accurate

knowledge of the shape of the individual vertebrae is also important for spinal biopsies, implants,

or the insertion of pedicle screws in spinal surgery [50]. However, manually delineating and

annotating vertebrae is a subjective, tedious, and error prone task. Preparing an automatic

vertebra segmentation system would greatly improve the process, thereby easing the workload

on radiologists while also removing operator variability.

Vertebra segmentation in CT images is a challenging task due to the presence of image artifacts,

contrast variations, presence of neighboring structures, and shape variation [50]. Recently, a

considerable amount of work has been done toward preparing automatic systems for detection

and segmentation of vertebrae. In this work, we mainly focus on comparison of the level set

segmentation with willmore flow and statistical shape modeling to compare the segmentation

results. In the following, we start by preparing a brief review on state-of-the-art regarding the

segmentation step. In Sec. 2, we explain in detail review of segmentation methods. In Sec. 3, we

prepare qualitative and quantitative results of these methods and compare the results achieved by

them.

2. LITERATURE SURVEY

Various attempts have been made at spine segmentation in recent years, but majority of them use

2-D images and/or require user intervention in the process. For example, Naegel [2] combined

the watershed method and morphological approaches to segment vertebrae. Although the

proposed method is promising in segmenting healthy bones from high-resolution images, manual

refinement is necessary to obtain accurate segmentations, and the level of refinement is patient

and resolution dependent. Ghebreab and Smeulders [3] constructed a deformable integral spine

model to segment vertebrae. The method learns the appearance of vertebrae boundaries a priori

from a set of training images. This model is then used to generate landmark points, in order to

reduce the complexity of the segmentation process through point-based shape representation.

However, it remains unclear if the landmark points correspond to the actual anatomical locations

and whether they capture the biologically meaningful variations across different subjects. The

method is also not fully automated and needs step-by-step inputs from the user, which makes the

whole process tedious and time consuming. Ma et al. [4] presented an automatic vertebra

segmentation and identification method on thoracic vertebra CT images. A learning-based bone

structure edge detection algorithm was used and a hierarchical, coarse-to-fine deformable

surface-based segmentation method was proposed based on the response maps from the learned

edge detector. Though satisfactory results were obtained, the segmented vertebrae were only in

2-D and reproducibility of results in 3-D was not known. Another limitation is the complexity

and/or inaccuracy of current segmentation methods. For example, Lorenze and Krahnstoever [5]

proposed a statistical shape model whereby the mean shape was constructed from a set of

training samples. The initialization of the shape model for segmentation was done manually and

is highly sensitive to dislocation. If the model is not located in the proximity of vertebrae,

segmentation may fail. More recently Klinder et al. [6] used a mesh-based method to extract

spine curves, and then generalized Hough transform and curved planar reformation to detect the

vertebrae. The proposed approach has a further identification step to the detected vertebrae via

rigid registration of appearance model. Although they achieved very competitive identification

rates for vertebrae, their algorithm depends heavily on spatial registration of the model, which is

computationally very expensive. In a paper by Mastmeyer et al. [7], a hierarchical 3-D technique

was developed to segment the vertebral bodies in order to measure bone mineral density. The

proposed framework needs excessive user intervention to precisely locate seed points to facilitate

region growing segmentation. This process is time consuming and impractical for unhealthy

bone segmentation. A similar approach integrating region growing segmentation with local shape

and intensity refinement for delineating vertebrae was proposed by Kang et al. [8]. First, locally

adaptive thresholds were used to facilitate region growing segmentations globally, followed by

3-D morphological operations to refine the segmented surfaces. This method still required a site

specific separation of individual bones, which remains a challenge for vertebrae segmentation.

Due to the aforementioned drawbacks of the existing spinal vertebrae segmentation methods, we

have developed a new method capable of segmenting spinal accurately from noisy images with

missing information. The method is developed by introducing an edge-mounted Willmore flow,

as well as a prior shape kernel density estimator, to the level set segmentation framework. While

the prior shape model provides much needed prior knowledge when information is missing from

the image, the edge-mounted Willmore flow helps to capture the local geometry and smoothes

the evolving level set surface.

The level set method [10] has been widely used for image segmentation [11]. The level set

segmentation obtained good results for highly challenging segmentation tasks, such as medical

images, level set methods have achieved good results when coupled with prior knowledge or

prior shape models [12][15]. The level set method embeds an interface in a higher dimensional

function (the signed distance function) as a level set = 0. The equation that governs the

evolution of the level set function (t) is /t + F|| = 0, where F represents the speed

function. In more recent development, the variational framework is often considered. Under the

variational framework, an energy E() is defined in relation to the speed function, and

minimization of the energy generates the EulerLagrange equation and, hence, providing the

evolution equation through the calculus of variation

E ()

=

t

To improve the results of level set segmentation we consider the fusion of energy, i.e., using a

shape prior distribution estimator Es with an edge-mounted Willmore energy Ew0

E ( )=Es+ E 0

where (0 < 1) is the weight parameter. Details on Es and Ew0 will be described in the

following sections. In order to incorporate a prior dataset {1, 2, . . . , N }into the level set

segmentation framework, we adopt a shape dissimilarity measure based on the Kernel density

estimation (KDE) discussed by Cremers et al. [13]. This nonparametric distribution estimator

overcomes the two shortcomings of existing algorithms: 1) the assumption that the shapes are

Gaussian distributed, which is generally inappropriate when the number of training set is small,

and not practical for modeling shapes with high complexity and structure; 2) the shapes are

represented by signed distance functions, which constitute a nonlinear space that does not

include the mean.

2.1.1 Kernel Density Estimation

KDE is a nonparametric approach in statistics for estimating the probability density function of a

random variable. The underlying theory of KDE states that data with unknown statistical

distribution converge to its actual distribution as the number of samples approaches infinity. In

practice, KDE provides a fundamental smoothing estimator even with a small number of data

samples. In application with N samples of shape models, the density estimation is formulated as

a sum of Gaussian of shape dissimilarity measures d2 (H(),H(i)), i = 1, 2, . . .,N

1

P() e

N i=1

d (H ( ) , H (i ))

2

2

where H() is the Heaviside function, the shape dissimilarity measure [16][18] is

1

d 2 ( H ( ) , H ( i )) = (H ( )H ( i ) )2 dx

2

min d H ( i ) , H ( j)

N

1

2

=

2 i , j=1

Note that the L2-norm is invariant under translation and scaling with respect to the principal axis

of the shape. Hence, the shape dissimilarity measure d2 is also invariant under these

transformations when the prior shapes are normalized with respect to translation and scaling

accordingly [13].

The segmentation is obtained by maximizing the conditional probability of given image I

P ( /I )=

P ( I / ) P ()

p(I )

Since the negative logarithmic scale of the probability distribution P(|I) nicely defines an

energy that associates the evolution of with the minimization problem, the shape energy is

formulated as

Es () = log P(|I).

Hence, the variational with respect to becomes

i d2 ( H ( ) , H ( i))

E s i=1

=

2 2 i

i=1

Willmore energy is a function of mean curvature, which isa quantitative measure of how much a

given surface deviates from a round sphere. It has been applied to image inpainting, restoration

of implicit surfaces [19], [20], and to studies of the bending energy of biological cell membranes

as these cell membranes tend to position themselves to minimize Willmore energy [21].

Willmore flow is the gradient flow of Willmore energy.Willmore flow of a surface is the

evolution of the surface in time to follow variations of the Willmore energy. Willmore energy

was defined after the British Geometer T.Willmore [22] and is formulated as

E =

1

h2 dA

2M

here we integrate Willmore flow into the level set segmentation framework as a geometric

functional. Willmore energy is defined on the collection of level sets, and Willmore flow is

enabled by defining a suitable metric, the Frobenius norm, on the space of the level sets. The

Frobenius norm of an arbitrary matrix A = (aij )mn , coincides with the calculation for the

gradient decent. It is equivalent to the l2-norm (the Euclidean norm) of a matrix, More

importantly, it is computationally attainable comparing to l2-norm. As Frobenius norm is an

inner-product norm, the optimization in the variational method comes naturally. Based on the

formulation by Droske and Rumpf [23], Willmore flow or the variational form for the Willmore

energy with respect to .

In order to ensure that the smoothing effect of Willmore energy acts around the constructed

surface and does not affect adversely the edge of vertebrae, we propose to multiply the edge

indicator function

g ( I )=

1

2

1+| GI|

We classify the existing vertebra segmentation approaches to two main groups: i) the ones, which

do not consider shape prior information, and ii) the ones, which do. Regarding the first group, we

can point to the following works: Ghosh et al. [36] extract the vertebra border as high gradient

edges. Peng et al. [45] apply the Canny edge detector on 2D slices for vertebra segmentation.

Aslan et al. [33] utilize a level set algorithm for vertebra segmentation. However, these methods

[36,45,33] do not make use of shape prior knowledge. Therefore, they are vulnerable to leakage

and thus lead to less accurate segmentation results. Considering the second group, there exist

several vertebra segmentation methods which make use of shape prior information. Aslan et al.

[32] consider shape prior information in a graph cut-based framework. Ma et al. [33] propose a

template-based segmentation method. However, these methods only rely on mean shape

information and do not benefit from the principal modes of variation. Herring et al. [39] compute

a coarse segmentation by simple thresholding and then register it to a pre-computed vertebra

shape model. However, their method requires a manual initialization; similar to the works in

[44,49]. Klinder et al. [42] propose a modelbased segmentation approach using a region-based

appearance model, which includes variance information.

2.2.1 METHOD

The general pipeline of our method is shown in Fig. 1. The input to our system is a 3D CT image

of the spinal cord accompanied with vertebra-bounding box information. These bounding boxes,

which are represented by their center, orientation, and scale, can be estimated by applying a

vertebra body detection as proposed by Kelm et al. [41]. Combining our method with this

method would lead to a fully automatic vertebra detection and segmentation system which does

not require any user interaction. Our method combines statistical shape modeling (SSM) to

capture global vertebra shape information and machine learning (ML) to capture local

appearance-related prior information. We break down our method into two main steps: the

training step and the testing step. In the training step, we compute the SSM and the boundary

detector model. In the testing step, we make use of the trained models resulting from the

previous step to segment vertebrae in an unseen image accompanied with its vertebra bounding

box information.

The training step of our framework consists of four main steps: i) finding the mesh point

correspondences, ii) normalizing the meshes and volumes, iii) extracting the SSM, and iv)

learning the boundary detector. Note that we do the learning step on cervical (V1 to V5), thoracic

(V6 to V17), and lumbar (V18 to V22) parts separately, where Vi represents the vertebra number.

In Fig. 2(b) the vertebrae inside the cervical, thoracic, and lumbar parts are represented by pink,

green, and orange, respectively.

Since extracting a SSM requires a set of training shapes with well-defined correspondences [38],

we apply a spectral-based algorithm to compute the point correspondences between the vertebra

meshes [40]. In the respective block in Fig. 1, corresponding points between a pair of meshes are

represented with the same color. Note that in our implementation of finding mesh-point

correspondences, we use vertebrae V3, V12, and V20 of one patient in the training set as the

reference meshes for cervical, thoracic, and lumbar parts and register all other meshes of each

group to them.3.1.2. Normalizing Meshes and Volumes The next step as depicted in Fig. 1 is

performing spatial normalization on the vertebra volumes and meshes. Regions within the

bounding boxes are spatially normalized to image volumes with equal size, resolution, and

orientation. The spatial normalization step is important in our machine learning-based approach.

Extracting 3D steerable features from these normalized volumes simplifies learning due to more

stable appearance patterns of the vertebra edges. A similar normalization step has beed proposed

by Wels et al.[47] to extract local features from vertebral bodies for spinal bone lesion detection.

We apply the same normalization step (normalizing w.r.t the box information) to the meshes. The

normalized meshes are used for extracting the SSM, as explained in the following.

After finding correspondences and normalizing the meshes, we apply Generalized Procrustes

Analysis (GPA) [37] to align the meshes rigidly. Let us represent aligned meshes by x1; x2; :::;

xN, N N+, where xi consists of the spatial coordinates of the surface points of the meshes.

N

Xi/ N ,

i=1

x i x

x i x

S=

i =1

(eigenvectors) and their respective variance _m (eigenvalue). Based on the main concept of SSM

theory, each shape in the training dataset can be approximated by a linear combination of the first

x x Pb

(1,...., m)

, where P =

is the

are the shape parameters [4].

2.2.5. Learning the Boundary Detector

To learn the boundary detector, given the normalized meshes and volumes, the image voxels on

the mesh surface are interpreted as positive training samples. Then, a set of 3D steerable features

is extracted from the points on the surface [50]. The same set of features is extracted from

several neighboring sampling points along the normal line of the mesh surface points providing

negative training samples [50,48]. These feature vectors are used to train the boundary detector

using a Probabilistic Boosting-Tree Classifier [50,48].

2.2.6 Testing Step

Given an unseen image with its vertebra bounding box information, we first spatially normalize

the volumes inside the box. On the normalized volumes, an initial estimation of the shape of the

x

xx

vertebra x is estimated using the computed mean shape ,i.e.,

. Then, a set of steerable

features is extracted from the mesh points x and several neighbouring sampling points along the

normal line of the mesh-surface points. After applying the boundary detector to the extracted

feature vectors, x is updated by a displacement vector

. To

x x x

and projected such that it can be approximated by the mean shape and a linear combination of

eigenvectors [4] (see Sec. 2.1.3).

As shown in Fig. 1, the final estimation of all the vertebrae in the original image space is made

by projecting back the detected meshes in the normalized space to the original image space.

3. OBJECTIVE

Proposed research objectives are as follows,

a) Implementation of willmore flow level set segmentation and statistical shape modeling

on vertebral CT images.

b) Selecting the most suitable one for further analysis using following parameters,

1. Prior shape energy.

2. Average measurement

3. Sensitivity, Specificity and Dice Similarity Coefficient.

c) Testing of the better algorithm on vertebral MRI images.

4. METHODOLOGY

CT IMAGES OF VERTEBRAE

SEGMENTATION OF VERTEBRAE

USING WILLMORE FLOW LEVEL

SET SEGMENTATION

SEGMENTATION USING

STSTISTICAL SHAPE MODELING

IMPLEMENTATION OF

BETTER ONE ON MRI IMAGES

OF VERTERBRAE

Image segmentation, is widely used in content based image retrieval, Machine vision, Medical

Imaging ,Object detection, Pedestrian detection, Face detection, Brake light detection, Locate

objects in satellite images, Recognition Tasks, Iris recognition, Traffic control systems. The main

applications of medical imaging are Locate tumors and other pathologies, Measure tissue

volumes, Diagnosis & study of anatomical structure. Medical imaging which consists mainly

combination of sensors recording the anatomical body structure like magnetic resonance image

(MRI), ultrasound or CT with sensors monitoring functional and metabolic body activities like

positron emission tomography (PET), single photon emission computed tomography (SPECT) or

magnetic resonance spectroscopy (MRS). Results can be applied, for instance, in radiotherapy

and nuclear medicine. This project mainly deals with the application on CT image on spinal

vertebrae.

Segmentation is often the key step in interpreting the image. Image segmentation is a process in

which regions or features sharing similar characteristics are identified and grouped together.

Image segmentation may use statistical classification, thresholding, edge detection, region

detection, or any combination of these techniques. The output of the segmentation step is usually

a set of classified elements. Most segmentation techniques are either region-based or edge based-

neighboring pixels. The cluster is referred to as the region, and the goal of the segmentation

algorithm is to group regions according to their anatomical or functional roles. Edge-based

techniques rely on discontinuities in image values between distinct regions, and the goal of the

segmentation algorithm is to accurately demarcate the boundary separating these regions.

Segmentation is a process of extracting and representing information from an image is to group

pixels together

In order to compare willmore flow level set segmentation with statistical shape model we create

a dataset of 20 ct images of normal spinal vertebrae images of patients. These images are

carefully selected by radiologists to form a representative group. The ground truths are obtained

by using TURTLESEG, 3D image segmentation software and verified by radiologists.

The willmore flow level set segmentation and statistical shape model are applied on these set of

images differently. a qualitative comparison between the segmented results are done between

these two models and analyze the better suited model.

For a quantitative evaluation we measure the errors of the segmented meshes from the model

which is better than other and try to implement the same on similar MRI images.

5.POSSIBLE OUTCOMES

Comparative results of willmore flow level set segmentation and statistical shape model

Better segmentation results for diagnosis

A method of segmentation for MRI images.

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