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Brain Tumor detection, Segmentation and 3D Reconstruction from MR Images


Muhammad Sultan Zia

PhD: 08-0988

SUPERVISED BY: DR. M. Arfan Jaffar

Department of Computer Science,

November 2010.


Problem Definition:

Magnetic Resonance Imaging (MRI) is a medical imaging technique used in radiology to visualize the internal structure of the body noninvasively. MRI provides rich information about human soft tissues anatomy. Segmentation and three-dimension modeling/reconstruction are the tools allowing a diagnostics automation and as well will assist the expert in the qualitative and quantitative analysis. It s an important step in various applications such as visualization, quantitative analysis and image-guided surgery. 3D segmentation of pathology and healthy structures is extremely important for surgical planning, qualitative and quantitative analysis such as volume measurements. The purpose of this research work is to facilitate the experts in above mentioned fields and surgeons to easily visualize the brain MR images of patients and certainly detect the region of tumor in the brain MR image. This is a very critical task. Wrong tumor region identification can lead to serious results. So accuracy in brain image processing and 3D modeling is very important concern. Brain is very complex in its structure. Moreover, accurately classifying it into accurate regions is very complex and sensitive task.

Image Segmentation plays a crucial role in many medical imaging applications by automating or facilitating the delineation of anatomical structures. Image segmentation is a process of partitioning an image into different homogeneous regions, so that meaningful information about the image can be obtained and different analysis can be performed on that segmented image. There are three tissue classes of brain that is gray matter (GM), white matter (WM) and cerebrospinal fluid (CSF). Accurate segmentation of these tissue classes is a vital step for brain image processing. The fundamental aspect that makes segmentation a difficult problem is the complexity and variability of the anatomy that is being imaged. After segmentation the accurate boundary detection is required so that an accurate 3D volumetric model can be constructed.

Before segmenting an image, First phase of brain tumor identification is to extract features from the brain MR image. Feature extraction efficiently specifies the boundaries between the brain structures to be identified e.g. brain tissues as well as ventricles. On the bases of these features images are classified as tumorous or non-tumorous. Segmentation will be used to distinguish the regions corresponding to different tissue types. Finally, the segmented regions will be labeled accordingly. These features help for identification of brain tumor region from brain MR images.

Precise segmentation of pathological structures is a difficult task because brain tumors vary greatly in size and position may have overlapping intensities with normal tissue and may be space occupying. Traditionally, the boundary of a tumor in magnetic resonance imaging is usually traced by hand. Then the practitioner is confronted with a succession of boundary which he mentally stacked up to be made a 3D representation of the tumor [1]. This reconstruction is inevitably subjective and becomes infeasible when dealing with large data sets, there is also an

information loss in all the in three-dimensional images directions and then the process is time- consuming and very difficult.

2. Objective:

This research work focus on brain MR image processing and 3D modeling using computer graphics and mathematical tools. The key objective of this research work is to build an automated system that automatically performs brain MR image processing for identification of tumor regions from brain MR images and then the 3D reconstruction of tumor volume brain volume and skull volume. The main focus of this research work is to first find the features from brain MR image and classification on the basis of these features. After classification segmentation is used to segment the different regions of brain MR image such as tumor, brain etc. At the end last phase is detection of boundaries and 3D reconstruction by using mathematical and computer graphics techniques.

First in this research work a literature review will be performed in which different proposed technique for brain MR image would be thoroughly studied .In this research work different proposed technique would be tested for feature extraction, classification and segmentation. After the analysis of these popular techniques, this research work will proposed a new technique for brain MR image processing which optimistically yields better results than all other proposed techniques for brain image processing. And finally 3D volumetric reconstruction is performed to visualize the different parts of brain MR images quantitatively and volumetrically by using computer graphics and mathematical tools.

3. Literature Review:

Zhang proposed a Hidden Markov Random Field Model and the Expectation-Maximization algorithm for segmentation of brain MR images [5]. This is a fully automatic technique for brain MR images segmentation. This method is based on estimation of threshold that is heuristic in nature. Thus most of the time, this method does not produce accurate results. Method in [5] is also computationally very expensive. Bin Li proposed membership constraint FCM algorithm by incorporating spatial information for image segmentation [6]. This proposed algorithm is quite similar to conventional FCM algorithm but it gives improve results for MR images on different noise level as compared to original FCM algorithm because it considers spatial information of MR images as well. T.Bala used wavelets coefficient for segmentation and a fuzzy clustering method for classification [7]. T.Bala et al [7] measures strength of clusters using silhouette method. M.Masroor proposed segmentation of brain MR images for tumor extraction by combining Kmeans Clustering for grouping tissues and Perona-Malik Anisotropic Diffusion Model [8] for image enhancement. This method also yields good results for segmentation. Ping proposed modified FCM algorithm by modifying membership weighting of every cluster and integrating spatial information [9]. Ping et al[9] applied this method on different MR images and their technique gives appropriate results for MR images of different noise type as compared to

standard FCM algorithm. Hassan Khotanlou etal [2] propose a general method for segmenting brain tumors in 3D magnetic resonance images. their method is applicable to different types of

tumors. Sandra Rua Ventura et al [3] proposed a 3D model for tongue.

Sripama proposed fuzzy symmetry based genetic clustering technique [10] for MRI brain image segmentation. In [10] numbers of clusters are evolved by variable length genetic fuzzy clustering technique. For measuring quality of cluster fuzzy point symmetry based cluster validity index is proposed in this paper. Experiments are performed on different T1, T2 and PD brain images. This technique performs better then FCM and Expectation Maximization algorithm. But this technique does not consider spatial information and sometime does not segment brain image correctly. This technique also does not work properly for the data sets which have same point as a center for different clusters. Yang proposed a denoising method that is a combination of total variation minimization and wavelet technique [11] for medical images. This method removes noise from noisy medical images without losing the sharpness of objects.

4. References

[1]. K. Aloui, and M. S. Naceur, 3D Brain Tumor Segmentation Using Level-Sets Method and

Meshes Simplification from Volumetric MR Images , World Academy of Science,

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[2]. Hassan Khotanlou, OlivierColliot, JamalAtif, IsabelleBloch, 3D brain tumor segmentation

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[3]. Sandra Rua Ventura, Diamantino Rui Freitas and João Manuel R. S. Tavares, THREE-


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[5]. Yongyue Zhang, Michael Brady, and Stephen Smith, Segmentation of Brain MR Images

Through a Hidden Markov Random Field Model and the Expectation-Maximization

Algorithm , IEEE Transaction on Medical Imaging, vol.20, No. 1, pp. 45-57, Jan 2001.


Bin Li, Wufan Chen, Dandan Wang, "An Improved FCM Algorithm Incorporating Spatial


Information for Image Segmentation,", 2008 International Symposium on Computer Science and Computational Technology, iscsct, vol. 2, pp.493-495,2008 T.Bala Ganesan, R. Sukanesh, Segmentation of Brain Images Using Fuzzy Clustering


Method with Silhouutte Method , Journal of Engineering and Applied Sciences, Medwell Journals ,pp.792-795, 2008. M. Masroor Ahmed ,Dzulkifli Bin Mohamad, Segmentation of Brain MR Images for

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