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1044931 Mikael Montelius Rapporten Utan Kod

Oct 22, 2014

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GTEBORG UNIVERSITY

M.Sc. Thesis

Matlab tool for segmentation and re-creation of 1 H-MRS volumes of interest in MRI image stacksMikael Montelius

Supervisors: Maria Ljungberg, Ph.D. sa Carlsson, Ph.Lic. DEPARTMENT OF RADIATION PHYSICS GTEBORG UNIVERSITY GTEBORG, 2008

AbstractIn in vivo Magnetic Resonance Spectroscopy (MRS) of the brain it is important to know the relative tissue volume of the volume of interest (VOI) specified in the measurement. In this project a tool for evaluating these relative tissue volumes was implemented in Matlab code. The program will be used in an MRS study of Obsessive Compulsive Disorder (OCD). The tool was programmed to allow interactive segmentation of the Magnetic Resonance (MR) images used when planning the VOI from where the MRS signal was extracted. The tool was also programmed to recreate and superimpose the VOI in the image stack and the accuracy of the positioning was tested in a phantom study. A PMMA (PolyMethyl MethAcrylate) cube was used as a phantom and was scanned in several MR scanners at Sahlgrenska University Hospital. The VOI was planned to coincide with the signal lacking cube, and an MRS spectrum was created to export the VOI settings from the scanner. The images and VOI settings were run through the tool and this produced a very good match between recreated VOI and the signal lacking PMMA cube. This was repeated for several phantom angulations and all results were equally good. Orthogonal image stacks which were recreated from the scanned images were also run through the tool with the same good result. Six series of volunteer measurements were performed following the OCD study routine to test the repeatability of the tool and the ability to create the same VOI position each time in in vivo MRS. The same volunteer was used all six times, and the resulting tissue ratios showed constancy over the series.

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AcknowledgementsI would like to express my gratitude to all those who gave me the possibility to complete this thesis. I am deeply indebted to my supervisors Maria Ljungberg and sa Carlsson for their patience and professional support and to Gran Starck for his technical advising. I would also like to thank the other co-workers and roommates at the department of MR and my classmates for an enjoyable time while producing this thesis. Especially, I would like to give my special thanks to my girlfriend Mia and all my family whose patient love enabled me to complete not only this project, but also my entire education.

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Nomenclature3D B0-field CHESS Cho Cr CSF DICOM FID FT Gln Glu GM in vitro in vivo Metabolite MR MRI MRS NAA OCD Precessional PMMA PRESS RF-pulse T1 T2 T2* TE TFE TI TMS TR VOI Voxel WM Three dimensional Static magnetic field of the MR scanner. Chemical Shift Selective (MR technique) Choline Creatinephosphocreatinine Cerebrospinal Fluid Digital Imaging and Communications in Medicine Free Induction Decay Fourier Transform Glutamine Glutamate gray matter Experiment outside a living organism, here phantom experiments Experiment on a living organism Molecule involved in metabolic process Magnetic Resonance Magnetic Resonance Imaging Magnetic Resonance Spectroscopy N-acetyl aspartate Obsessive Compulsive Disorder Rotating motion of spinning axis PolyMethyl MethAcrylate Point Resolved Spectroscopy (MRS pulse sequence) Radio frequent pulse Longitudinal, or spin-lattice, relaxation time constant Transversal, or spin-spin, relaxation time constant T2, including external factors, decreasing the relaxation time Echo Time Turbo Field Echo Inversion Time Tetramethylsilane Repetition Time Volume of interest Volume pixel white matter

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ContentsIntroduction ....................................................................................................................................6 1. Aim...........................................................................................................................................7 2. MR Basics................................................................................................................................7 2.1.1. Nuclear spin and energy states..............................................................................7 2.1.2. The Larmor equation.............................................................................................7 2.1.3. The Radio Frequency pulse and the Free Induction Decay ...............................8 2.1.4. Relaxation-, Repetition- and Echo Times ............................................................9 2.2. MRI................................................................................................................................10 2.2.1. Image construction...............................................................................................11 2.2.2. The turbo field echo sequence .............................................................................11 2.3. MRS ...............................................................................................................................13 2.3.1. Spectroscopy .........................................................................................................13 2.3.2. The Chemical Shift...............................................................................................14 2.3.3. J-coupling..............................................................................................................15 2.4. Digital image matrices .................................................................................................16 2.4.1. Image histogram thresholding and segmentation .............................................16 2.4.2. The Binary Mask..................................................................................................18 2.5. Data Format..................................................................................................................19 2.6. Anatomy of the brain ...................................................................................................20 3. Material and methods ..........................................................................................................21 3.1. The Image Processing toolbox in Matlab...................................................................21 3.2. Determining the image and VOI coordinate systems ...............................................21 3.3. Partitioning the tool .....................................................................................................22 3.4. Segmentation.................................................................................................................22 3.5. VOI re-creation ............................................................................................................27 3.6. Verification of VOI re-creation...................................................................................33 3.7. In vivo verification of repeatability.............................................................................34 4. Results ...................................................................................................................................37 4.1. The image and VOI coordinate systems.....................................................................37 4.2. Segmented images ........................................................................................................38 4.3. VOI re-creation ............................................................................................................40 4.4. Verification of VOI re-creation...................................................................................42 4.5. In vivo verification of repeatability.............................................................................44 5. Discussion..............................................................................................................................49 6. Conclusions ...........................................................................................................................54 7. References .............................................................................................................................54 8. Appendix ...............................................................................................................................56 8.1. Maths .............................................................................................................................56 8.2. To make changes in the code.......................................................................................59 8.3. Experience based tool instructions. ............................................................................60 8.4. Matlab code reference..................................................................................................62

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IntroductionObsessive Compulsive Disorder (OCD) is an anxiety disorder characterized by the occurrence of repeated and distressing intrusive thoughts and compulsive actions performed to lessen distress [1]. The disorder is typically treated with behavioral therapy, cognitive therapy, medications, or any combination of the three. To better understand the disorder, researchers at Sahlgrenska University hospital use in vivo magnetic resonance spectroscopy (MRS) in clinical studies of the metabolite concentrations in parts of the brain believed to be affected [2]. The patient stays in the MR scanner during the whole examination and a survey MRI (MR Imaging) scan is performed to get an overview of the position of the patient. With the aid of this survey, the operator plans a 3D image stack or a multiple series of 2D images with better resolution to resolve the structure of the brain. From this image stack several reconstructions are made. These are rotated freely in three dimensions to better meet the criteria of the