Multimodal image registration is essential when combining functional and structural imaging modalities. Among the most common combinations, numerous methods have been developed for co-registration of CT and PET, typically validated on human size scanners. However, only a few registration studies have been performed for the combination of small animal miniPET and microCT imaging. The Jonasson Center for Medical Imaging at KTH possesses an integrated miniPET/ microCT for pre-clinical research purposes. The motivation for this work is the need for the development of fusion method(s) for combining the data of these two modalities. In this work, a novel pipeline registration method, employing image processing and Mutual Information (MI) is proposed and implemented. The method starts with a pre-alignment step before acquisition of the miniPET/microCT volumes, followed by scaling, binarization and processing of the two volumes and finally, a registration procedure by Maximization of Mutual Information (MIM) as a voxel-based similarity metric. A established intrinsic landmarks based method is also implemented for comparison. For the validation of the methods, volumes acquired by in-house designed 3D printed Polyethylene (PE) phantoms, filled with multiple concentrations of FDG were used. The misalignment between corresponding points volumes after registration, is analyzed and compared in terms of absolute spatial distance. The proposed method based on 3D processed volumes outperformed the Landmarks based registration method, showing average misalignments of 0.5 mm. The registered volumes were also successfully visualized together using Alpha blending. By so, an automatic fusion method for miniPET/microCT has thus been implemented, presented and evaluated, raising prospects for multimodal imaging research at the Jonasson Center for Medical Imaging. / Kombinationen av funktionell och strukturell avbildning är vanlig inom medicinsk bildgivning, och koregistrering av bildvolymerna utgör en essentiell del i den multimodala framställningen. PET/CT-avbildning hör till de vanligast förekommande multimodala avbildningskombinationerna, och till följd av detta har ett antal koregistreringsmetoder utvecklats för just detta. Vad gäller pre-klinisk avbildning är dock validerade koregisteringsmetoder inte lika vanliga, och framförallt inom forskningsbaserad avbildning (där egendesignade scanners förekommer) är behovet av effektiva metoder tydligt. Inom Jonassons centrum för medicinsk avbildning på KTH har ett multimodalt miniPET/ microCT-system utvecklats, och det är just behovet av koregistering som utgjort basen för följande examensarbete. I följande arbete har en koregistreringsmetod baserad på fördefinierad bildbehandling och analys av gemensam information (mutual information, MI) implementerats och testats. Metoden bygger på ett initialt upplinjeringssteg innan microCT/ miniPET bildtagning. Efter detta genomförs en rad bildbehandlingssteg (skalning, binärisering) innan en slutgiltig koregistrering genomförs med hjälp av s.k. maximering av gemensam information (Maximization of Mutual Information, MIM). En etablerad landmärkesbaserad metod implementerades även som jämförelse. Metoderna testades sedan genom multimodal avbildning av egendesignade 3D-printade fantomer, fyllda med varierande aktivitet av FDG. Den föreslagna MI-metoden överträffade den etablerade landmärkesmetoden, med ett genomsnittligt koregistreringsfel på 0.5 mm. Visualisering av de koregistrerade volymerna genomfördes även genom så kallad alpha blending. Genom detta har en koregistreringsmetod för miniPET/microCT:n på Jonassons center för medicinsk avbildning implementerats och testats, vilket möjliggör för framtida studier av multimodal avbilning på KTH.

The main goal of the project was to compare how the Achilles tendon is affected while running with traditional shoes, minimalistic shoes and barefoot. Displacement and strain were calculated both for different shoes and for different foot strike patterns. The calculations were done with a speckle tracking algorithm and displacement was calculated for three different depths in the tendon: deep layer, mid layer and superficial layer. The goal was also to conduct this analysis after a review of the algorithm used. The review of the algorithm focused on the size of the region of interest, kernel size and frequency. Literature study showed that it is more common to use a smaller kernel size, but the same shape. The region of interest was chosen depending on the size of the tendon. Displacement and strain in the Achilles tendon was calculated for seven subjects and the result did not show any difference in amount of mean deformation due to different shoe types or foot strike patterns. It was a small sample group but the result indicated a difference in peak displacement between deep and superficial layer depending on different shoe types and foot strike patterns. The difference in peak displacement between deep and superficial layer was lowest when running barefoot, larger when running with minimalistic shoes and greatest when running with traditional shoes. This result was only achieved when running with rear foot strike pattern. When running with fore foot strike pattern the difference in peak displacement between layers did not change with different conditions. In all conditions the difference in peak displacement between the layers was greater when running with rear foot strike pattern than when running with front foot strike pattern. The deep layer displaced more than the superficial layer (p<0.01) for all conditions and foot strike patterns.

The harmonic generation due to the nonlinear behavior of Ultrasound Contrast Agents (UCAs) must be exploited for improved efficiency when imaging vascular targets in the neighborhood of highly echogenic tissue. One may even further improve the efficiency by focusing on the subharmonic generation of the UCAs, which is an even more exclusive property than the generation of higher harmonics, for improved Contrast-to-Tissue ratio (CTR). The aim of this work was first, the design of a set-up for nonlinear imaging of Poly-Vinyl Alcohol (PVA) based UCAs on The Verasonics Research System with special focus on nondestructive Subharmonic Imaging. The second part of the work addressed the evaluation of the subharmonic response provided by the agents in the developed setup. Six different imaging techniques were developed. These were Fundamental B-mode imaging (FB), Pulse Inversion imaging (PI), and a Contrast Pulse Sequence based on three pulses (CPS3), with and without a focus on the subharmonic component by the implementation of a Linear Bandpass Filter (LBF). Experiments were performed on a tissue mimicking flow phantom and the performance of the agents for each technique was determined in terms of CTR and CNR. The PVA agents provided a backscattering enhancement of the order of 23 dB through FB imaging. However, the performance of the FB technique was unsatisfactory in terms of CTR. The CPS3 sequence performed best of the six techniques with an improvement of 14 dB and 13 dB in CTR and CNR, respectively, compared with the FB technique. Combining the LBF around the subharmonic component with the multi-pulse techniques of PI and CPS3 resulted in a degraded CTR performance due to significant amount of signals from tissue around the subharmonic component and insufficient subharmonic detection from the PVA agents.

Motor intent and control rely on complex high-level and spinal networks. Untilnow, little is known about this system’s organization and mechanisms. Whilecognitive abilities play an essential role in planning movements, learning andmemorizing, their involvement during stereotyped tasks execution, aslocomotion, is still controversial. Recently, the relationship between cognitivefunctions and gait has received increasing attention.Here, a machine learning approach is used to investigate the engagement ofdi↵erent cortical areas during motor activity. In particular, data coming fromthree subjects with implanted electrodes have been analyzed in the frequencydomain to predict their tasks’ state. The choice of intracortical data hasallowed to elude motion artifacts’ presence and exploitation concern. Goodand satisfactory results have been achieved in the case of not highlystereotyped activity. During ambulation, an evidence of an engagement of thebrain has been shown even if with lower classification performances. Moreover,the cortical areas that have emerged in this analysis seem to be in line withthe relative functionality hypothesized in literature.

This project revolves around the measurement of T1 and T2 relaxation times in the ratbrain, in a multi-center way. That is to say, elaborate an efficient protocol to calculate highresolution 3D map of the brain. This protocol should be applied in different centers andreturn similar results. Finally, procedures should be defined to ease the collaborationbetween the different centers. The first step consisted in in vitro experiments, in whichdifferent sequences were tested. It resulted that the MDEFT sequence with inversionpreparation (MPRAGE) gives the best results in the shortest time for T1. For T2, theMSME sequence was chosen. The next step moved on in vivo experiments on three rats inorder to get used to manipulating living animals and make new adjustments. As thephysiology is not the same on in vitro and in vivo experiments, some parameters had to beslightly adapted. Once the final 2h-protocol was established, it was tested on a populationof ten rats. Experiments were made at the GIN and CRMBM. Different fitting pipelineswere tried (GIN, CRMBM, MIRCEN). The brain was segmented into different regions. Itresulted that the GIN and CRMBM pipelines return the same T1 values using the differentdatasets. The MIRCEN pipeline under-estimates by 200 ms. The three pipelines return similar T2 values. The GIN and CRMBM datasets provide comparable T1 values, but theGIN center presents slightly higher T2 values. Regarding the multi-center collaboration,the different pipelines were ported to the VIP platform so that the scientific community caneasily reuse them.

Muscle driven devices are controlled or powered with muscle activation. These devices open up the possibility of offering patients with limited muscle function to automatically control assistive devices - for instance exoskeletons - with input from their own muscles. This solution would help a number of patient groups suffering from common conditions, such as spinal cord injuries, stroke and cerebral palsy. To use muscle activation as input it is necessary to have a way to communicate with the mus- cles. Electromyography (EMG) is a technology used to gain information about muscle function and activation. It is performed by measuring and analyzing electrical signals conducted by the muscles during activation. Activation and activation level can be seen from analyzed EMG signal. EMG signals are frequently measured and analyzed afterwards, however, to use it as a controlling an assistive devices, real time analysis is necessary. In this thesis real time acquisi- tion and analysis of EMG was performed. The measured signal was used as an input to control a simple MATLAB computer game. The EMG of a muscle of the forearm, Brachioradialis, was measured with Myon Aktos sys- tem. The measured signal was written to a server as soon as the measurements were acquired. MATLAB was used to connect to the server and performing the signal analysis. The analysis was kept simple in order to limit delay. The result showed that it was possible to acquire real time signal with this method. The delay was negligible, both for the testing and for the game play. Showing that it is possible to play a game with muscle activation supports the idea of a motor that can be controlled automatically with muscle input. Future work should focus on understanding movement intent with respect to EMG and on analyzing multiple signals from different muscles at the same time.

Background: Individuals with cerebral palsy (CP) are prone to sedentary life with limited recreational- and physical activity. RaceRunning (RR) is a sport for individuals with disabilities such as motor impairment that allow them to move independently and enjoy physical activity. The aim of the study was to investigate muscle fatigue of RR athletes with different classiffcation of CP during six minuteRaceRunning test (6MRRT). The Cerebral Palsy International Sports and RecreationAssociation has the goal to make RR a Paralympic sport. For a sport to be included in the Paralympics a classiffcation system has to be made. Information about muscle function during RR could give vital physical information about athletes with CP and contribute to the development of such classiffcation system. Method: Median frequency of the power spectrum from surface electromyography(sEMG) of four muscles (vastus lateralis, biceps femoris, gluteus medius, gastrocnemius lateralis) was computed along with amplitude changes (root mean square) in order to assess muscle fatigue. Results: Indications of muscle fatigue were observed from one out of five athletes for athlete's less affected side. Further sEMG studies with more subjects have to be conducted on CP RR athletes to give more conclusive results of muscle fatigue.

The induced rupturing of Poly Vinyl Alcohol (PVA) microbubbles with high mechanical index (MI)ultrasound beam is used in multiple medical application such as drug delivery, image contrastenhancement and perfusion imaging.In this work, Triggered imaging technique with subtraction algorithm is used to enhance themicrobubble’s (MB) contrast over tissue (CTR). The technique is performed by rupturing MBwith one destruction wave sequence followed by 100 B-mode imaging pulse sequences. Theimages obtained are then subtracted by a base image that is selected after the destruction pulse[1].The result of this technique depends mainly on the effectiveness of destruction pulse inrupturing highest number of MB. This has been tested through tissue mimicking phantomwithout replenishing the MB. The evaluation of the methods is done through the CTR and CNRcalculation for each of the 100 frames.The contrast enhancement technique used has also been tested with similar setup but withcontinuous replenishment of MB. The evaluation is done by comparing CNR and CTR results forthe 100 frames obtained by B-mode imaging with the ones resulted from the subtractionalgorithm.The contrast values obtained from both experiments are used in driving the characterization ofPVA response to high MI.The result for the destruction pulse effectiveness shows that the pulse indeed managed toreduce number of MB, but not to the lowest. This is because of leaked gas from cracked shell,the shell acoustic enhancement effect, and large bubbles which managed to survive.The Triggered imaging has shown large improvement in CTR value with use of the subtractionalgorithm when compared to B-mode results. In addition, it has provided an experimental wayfor perfusion imaging and quantification by monitoring CTR value after the destructive pulse[2]. This sets the bases for experimental research relevant to tissue perfusion at ultrasound labof KTH.

This study investigates the in-vivo architecture of muscles in the lower leg using 2D ultrasound (US) and 3D diffusion tensor imaging (DTI) techniques. The muscle architecture of the gastrocnemius, posterior soleus and tibialis anterior were compared using US and DTI imaging. DTI and US differed on average by 17% in fascicle length (FL), 20% in muscle thickness (tm), and 36% in pennation angles (PA).The study furthermore examined the muscle morphology after stroke by comparing the muscles of the affected side to the less-affected side of five hemiplegic post-stroke patients. The morphology of eight muscle compartments in both legs of the patients was measured using only DTI. An, on average, 14% smaller muscle volume in the effected side was found, as well as a difference of 15% in FL, 11% PA, and 17% in physiological cross-sectional area (PCSA). However, changes in FL, PA and PCSA were not only observed between sides but also differed among muscle compartments. The parameter values were in general in the range of human subjects but no conclusive differences between sides could be found based on the acquired data. In conclusion, DTI and US both yielded results of muscle architecture parameters within a physiologically range but can differ substantially between methods and cannot be compared directly.

Metal-on-polymer prostheses in orthopaedics are often subject to high wear level producing large polyethylene particles that the body has difficulties to eliminate. Those debris can lead to prosthesis loosening. This study investigates the wear behaviour of TA6V, a CoCr alloy, M30NW and 316L stainless steels against UHMWPE on a pin-on-disc tribometer under lubricated conditions. Friction coefficient of 316L showed an inflection in their rise while the increase of others was linear. 316L also produced the most friction and wear. On the contrary, CoCr confirmed its good properties. Both stainless steels showed similar behaviour and metal manufacturing process only modified UHMWPE loss and not the wear rates.