Adipose tissue volume and distribution is related to metabolic diseases such as diabetes and atherosclerosis. This relationship is in focus for much research, much due to a worldwide increase in obesity. It is in many cases of interest to calculate the amount of adipose tissue in different compartments within the body. Commonly used methods are however prone to introduce errors due to partial volume effects. Previous studies have successfully segmented three adipose tissue compartments from abdominal two-point Dixon fat-water MRI volumes using Morphon registration and atlas segmentation. This thesis extends upon the previous work by enabling segmentation of whole-body MRI volumes and by improving the registration with the use of both fat and water data. Possible methods for bone marrow segmentation are also tested and evaluated. The methods presented seem to be sufficient for creating whole-body volumes from a set of smaller volumes. The adipose tissue segmentation was adequate for subjects with relatively small volumes of adipose tissue, whereas segmentation of subjects with large amounts of adipose tissue require further improvement. Of the evaluated methods for bone marrow segmentation one seemed to perform adequately on all the tested datasets. Due to the few datasets available for testing it was not possible to draw any general conclusions as to how well the presented methods perform.

<p>Nukleärmedicinska bilder som exempelvis SPECT (Single Photon Emission Tomogra-phy) är en bildgenererande teknik som ofta används i många applikationer vid mätning av fysiologiska egenskaper i den mänskliga kroppen. En vanlig sorts undersökning som använder sig av SPECT är myokardiell perfusion (blodflöde i hjärtvävnaden), som ofta används för att undersöka t.ex. en möjlig hjärtinfarkt. För att göra det möjligt för läkare att ställa en kvalitativ diagnos baserad på dessa bilder, måste bilderna först segmenteras och roteras av en biomedicinsk analytiker. Detta utförs på grund av att hjärtat hos olika patienter, eller hos patienter vid olika examinationstillfällen, inte är lokaliserat och roterat på samma sätt, vilket är ett väsentligt antagande av läkaren vid granskning</p><p>av bilderna. Eftersom olika biomedicinska analytiker med olika mängd erfarenhet och expertis roterar bilderna olika uppkommer variation av de slutgiltiga bilder, vilket ofta kan vara ett problem vid diagnostisering.</p><p>En annan sorts nukleärmedicinsk undersökning är vid kvantifiering av dopaminreceptorer i de basala ganglierna i hjärnan. Detta utförs ofta på patienter som visar symptom av Parkinsons sjukdom, eller liknande sjukdomar. För att kunna bestämma graden av sjukdomen används ofta ett utförande för att räkna ut olika kvoter mellan områden runt dopaminreceptorerna. Detta är ett tröttsamt arbete för personen som utför kvantifieringen och trots att de insamlade bilderna är tredimensionella, utförs kvantifieringen allt för ofta endast på en eller flera skivor av bildvolymen. I likhet med myokardiell perfusionsundersökningar är variation mellan kvantifiering utförd av olika personer en möjlig felkälla.</p><p>I den här rapporten presenteras en ny metod för att automatiskt segmentera hjärtats vänstra kammare i SPECT-bilder. Segmenteringen är baserad på en intensitetsinvariant lokal-fasbaserad lösning, vilket eliminerar svårigheterna med den i myokardiella perfusionsbilder ofta varierande intensiteten. Dessutom används metoden för att uppskatta vinkeln hos hjärtats vänstra kammare. Efter att metoden sedan smått justerats används den som ett förslag på ett nytt sätt att automatiskt kvantifiera dopaminreceptorer i de basala ganglierna, vid användning av den radioaktiva lösningen DaTSCAN.</p> / <p>Nuclear medical imaging such as SPECT (Single Photon Emission Tomography) is an imaging modality which is readily used in many applications for measuring physiological properties of the human body. One very common type of examination using SPECT is when measuring myocardial perfusion (blood flow in the heart tissue), which is often used to examine e.g. a possible myocardial infarction (heart attack). In order for doctors to give a qualitative diagnose based on these images, the images must first be segmented and rotated by a medical technologist. This is performed due to the fact that the heart of different patients, or for patients at different times of examination, is not situated and rotated equally, which is an essential assumption for the doctor when examining the images. Consequently, as different technologists with different amount of experience and expertise will rotate images differently, variability between operators arises and can often become a problem in the process of diagnosing.</p><p>Another type of nuclear medical examination is when quantifying dopamine transporters in the basal ganglia in the brain. This is commonly done for patients showing symptoms of Parkinson’s disease or similar diseases. In order to specify the severity of the disease, a scheme for calculating different fractions between parts of the dopamine transporter area is often used. This is tedious work for the person performing the quantification, and despite the acquired three dimensional images, quantification is too often performed on one or more slices of the image volume. In resemblance with myocardial perfusion examinations, variability between different operators can also here present a possible source of errors.</p><p>In this thesis, a novel method for automatically segmenting the left ventricle of the heart in SPECT-images is presented. The segmentation is based on an intensity-invariant local-phase based approach, thus removing the difficulty of the commonly varying intensity in myocardial perfusion images. Additionally, the method is used to estimate the angle of the left ventricle of the heart. Furthermore, the method is slightly adjusted, and a new approach on automatically quantifying dopamine transporters in the basal ganglia using the DaTSCAN radiotracer is proposed.</p>

Nukleärmedicinska bilder som exempelvis SPECT (Single Photon Emission Tomogra-phy) är en bildgenererande teknik som ofta används i många applikationer vid mätning av fysiologiska egenskaper i den mänskliga kroppen. En vanlig sorts undersökning som använder sig av SPECT är myokardiell perfusion (blodflöde i hjärtvävnaden), som ofta används för att undersöka t.ex. en möjlig hjärtinfarkt. För att göra det möjligt för läkare att ställa en kvalitativ diagnos baserad på dessa bilder, måste bilderna först segmenteras och roteras av en biomedicinsk analytiker. Detta utförs på grund av att hjärtat hos olika patienter, eller hos patienter vid olika examinationstillfällen, inte är lokaliserat och roterat på samma sätt, vilket är ett väsentligt antagande av läkaren vid granskning av bilderna. Eftersom olika biomedicinska analytiker med olika mängd erfarenhet och expertis roterar bilderna olika uppkommer variation av de slutgiltiga bilder, vilket ofta kan vara ett problem vid diagnostisering. En annan sorts nukleärmedicinsk undersökning är vid kvantifiering av dopaminreceptorer i de basala ganglierna i hjärnan. Detta utförs ofta på patienter som visar symptom av Parkinsons sjukdom, eller liknande sjukdomar. För att kunna bestämma graden av sjukdomen används ofta ett utförande för att räkna ut olika kvoter mellan områden runt dopaminreceptorerna. Detta är ett tröttsamt arbete för personen som utför kvantifieringen och trots att de insamlade bilderna är tredimensionella, utförs kvantifieringen allt för ofta endast på en eller flera skivor av bildvolymen. I likhet med myokardiell perfusionsundersökningar är variation mellan kvantifiering utförd av olika personer en möjlig felkälla. I den här rapporten presenteras en ny metod för att automatiskt segmentera hjärtats vänstra kammare i SPECT-bilder. Segmenteringen är baserad på en intensitetsinvariant lokal-fasbaserad lösning, vilket eliminerar svårigheterna med den i myokardiella perfusionsbilder ofta varierande intensiteten. Dessutom används metoden för att uppskatta vinkeln hos hjärtats vänstra kammare. Efter att metoden sedan smått justerats används den som ett förslag på ett nytt sätt att automatiskt kvantifiera dopaminreceptorer i de basala ganglierna, vid användning av den radioaktiva lösningen DaTSCAN. / Nuclear medical imaging such as SPECT (Single Photon Emission Tomography) is an imaging modality which is readily used in many applications for measuring physiological properties of the human body. One very common type of examination using SPECT is when measuring myocardial perfusion (blood flow in the heart tissue), which is often used to examine e.g. a possible myocardial infarction (heart attack). In order for doctors to give a qualitative diagnose based on these images, the images must first be segmented and rotated by a medical technologist. This is performed due to the fact that the heart of different patients, or for patients at different times of examination, is not situated and rotated equally, which is an essential assumption for the doctor when examining the images. Consequently, as different technologists with different amount of experience and expertise will rotate images differently, variability between operators arises and can often become a problem in the process of diagnosing. Another type of nuclear medical examination is when quantifying dopamine transporters in the basal ganglia in the brain. This is commonly done for patients showing symptoms of Parkinson’s disease or similar diseases. In order to specify the severity of the disease, a scheme for calculating different fractions between parts of the dopamine transporter area is often used. This is tedious work for the person performing the quantification, and despite the acquired three dimensional images, quantification is too often performed on one or more slices of the image volume. In resemblance with myocardial perfusion examinations, variability between different operators can also here present a possible source of errors. In this thesis, a novel method for automatically segmenting the left ventricle of the heart in SPECT-images is presented. The segmentation is based on an intensity-invariant local-phase based approach, thus removing the difficulty of the commonly varying intensity in myocardial perfusion images. Additionally, the method is used to estimate the angle of the left ventricle of the heart. Furthermore, the method is slightly adjusted, and a new approach on automatically quantifying dopamine transporters in the basal ganglia using the DaTSCAN radiotracer is proposed.

Automatic segmentation of human organs allows more accurate calculation of organ doses in radiationtreatment planning, as it adds prior information about the material composition of imaged tissues. For instance, the separation of tissues into bone, adipose tissue and remaining soft tissues allows to use tabulated material compositions of those tissues. This approximation is not perfect because of variability of tissue composition among patients, but is still better than no approximation at all. Another use for automated tissue segmentationis in model based iterative reconstruction algorithms. An example of such an algorithm is DIRA, which is developed at the Medical Radiation Physics and the Center for Medical Imaging Science and Visualization(CMIV) at Linköpings University. DIRA uses dual-energy computed tomography (DECT) data to decompose patient tissues into two or three base components. So far DIRA has used the MK2014 algorithm which segments human pelvis into bones, adipose tissue, gluteus maximus muscles and the prostate. One problem was that MK2014 was limited to 2D and it was not very robust. Aim: The aim of this thesis work was to extend the MK2014 to 3D as well as to improve it. The task was structured to the following activities: selection of suitable segmentation algorithms, evaluation of their results and combining of those to an automated segmentation algorithm. Of special interest was image registration usingthe Morphon. Methods: Several different algorithms were tested.  For instance: Otsu's method followed by threshold segmentation; histogram matching followed by threshold segmentation, region growing and hole-filling; affine phase-based registration and the Morphon. The best-performing algorithms were combined into the newly developed JJ2016. Results: For the segmentation of adipose tissue and the bones in the eight investigated data sets, the JJ2016 algorithm gave better results than the MK2014. The better results of the JJ2016 were achieved by: (i) a new segmentation algorithm for adipose tissue which was not affected by the amount of air surrounding the patient and segmented smaller regions of adipose tissue and (ii) a new filling algorithm for connecting segments of compact bone. The JJ2016 algorithm also estimates a likely position for the prostate and the rectum by combining linear and non-linear phase-based registration for atlas based segmentation. The estimated position (center point) was in most cases close to the true position of the organs. Several deficiencies of the MK2014 algorithm were removed but the improved version (MK2014v2) did not perform as well as the JJ2016. Conclusions: JJ2016 performed well for all data sets. The JJ2016 algorithm is usable for the intended application, but is (without further improvements) too slow for interactive usage. Additionally, a validation of the algorithm for clinical use should be performed on a larger number of data sets, covering the variability of patients in shape and size.

Detection and positioning of anatomical landmarks, also called points of interest(POI), is often a concept of interest in medical image processing. Different measures or automatic image analyzes are often directly based upon positions of such points, e.g. in organ segmentation or tissue quantification. Manual positioning of these landmarks is a time consuming and resource demanding process. In this thesis, a general method for positioning of anatomical landmarks is outlined, implemented and evaluated. The evaluation of the method is limited to three different POI; left femur head, right femur head and vertebra T9. These POI are used to define the range of the abdomen in order to measure the amount of abdominal fat in 3D data acquired with quantitative magnetic resonance imaging (MRI). By getting more detailed information about the abdominal body fat composition, medical diagnoses can be issued with higher confidence. Examples of applications could be identifying patients with high risk of developing metabolic or catabolic disease and characterizing the effects of different interventions, i.e. training, bariatric surgery and medications. The proposed method is shown to be highly robust and accurate for positioning of left and right femur head. Due to insufficient performance regarding T9 detection, a modified method is proposed for T9 positioning. The modified method shows promises of accurate and repeatable results but has to be evaluated more extensively in order to draw further conclusions.