In recent years, researchers have increasingly used magnetic resonance imaging (MRI) to study temporal skeletal muscle changes using gradient echo (GRE) echo planar imaging (EPI). These studies, typically involving exercise or ischemic challenges, have differentiated healthy subjects from athletic or unhealthy populations, such as those with peripheral vascular disease. However, the analysis methodologies have been lacking. In this thesis, two sessions of post-exercise GRE EPI data were collected from six subjects' lower legs using a 3 Tesla MRI scanner and a custom built ergometer. Past studies used common medical imaging software for motion correction. This work shows that such tools degrade leg image data by introducing motion, increasing root mean squared error in rest data by 22%. A new approach decreased it by 12%. EPI distortion correction in muscle images was also achieved, with the correlation ratio of functional and structural images increasing by up to 8%. In addition, a brief but intense artifact in GRE EPI muscle images results from muscle tissue moving in and out of the imaged volume. This through-plane artifact was successfully modelled as a mono-exponential decay for regression analysis, increasing the utility of the residual signal. The regression parameters were also leveraged to produce muscle displacement maps, identifying 44% of voxels as displaced. The maps were validated in a motion phantom and in-vivo using ultrasound. Finally, independent component analysis (ICA) was applied to post-exercise GRE EPI images to detect features in a data-driven, multivariate way and improve on conventional ROI selection methods. ICA produced parametric maps that were spatially correlated to working muscles from every trial (most with |R| > 0.4). The components were also separated from the susceptibility, motion, and blood vessel signals, and temporally reliable within individuals. These methodological advances represent increased rigour in the analysis of muscle GRE EPI images. / Thesis / Doctor of Philosophy (PhD) / Adequate blood circulation to muscles is important for good health. Researchers have used magnetic resonance imaging (MRI) techniques to assess blood and oxygen supply to muscles. The work in this thesis improves upon the analysis methods in prior work, especially in the areas of motion correction of the images and selection of individual muscle regions for analysis. Previous techniques could sometimes make motion in muscle images worse. This work provides valuable motion and distortion correction for muscle imaging, ensuring that measurements truly reflect muscle physiology. It also describes a method to remove an unwanted signal from post-exercise muscle data, and create a map of the internal muscle motion that occurred. Finally, an advanced mathematical technique was used to extract signals of interest and important spatial features from muscle image data automatically. The technique produced reliable results within and among subjects.

Recent work has demonstrated improvement of image quality with low atomic number (Z) linear accelerator (linac) targets and energies as low as 3.5 MV compared to a standard 6 MV therapeutic beam. In this work, the incident electron beam energy has been lowered to energies between 1.90 and 2.35 MeV. The improvement of megavoltage planar image quality with the use of carbon and aluminum linac targets has been assessed compared to a standard 6 MV therapeutic beam. Common electronic portal imaging devices contain a 1.0 mm copper conversion plate to increase detection efficiency of a therapeutic megavoltage spectrum. When used in imaging with a photon beam generated with a low-Z target, the conversion plate attenuates a substantial proportion of photons in the diagnostic range, thereby reducing the achievable image quality. Image quality as a function of copper plate thickness has been assessed for planar imaging and cone beam computed tomography.

Biologists and physicians study complex biologic phenomena in which they use advanced imaging methods. They acquire images containing a lot of information which must be extracted in a correct way. This requires computer skills and knowledge in image processing methods which they seldom have. To overcome the problem, this master thesis aimed to develop a routine for artefact correction and information extraction from images acquired in a research project at the Karolinska Institutet in Stockholm. By developing the routine, the thesis showed how software developed for images of human can be applied to images of rats. The routine handles formatting issues and artefact corrections, calculates diffusion metrics, and performs statistical tests on spatially aligned magnetic resonance images of rats acquired with diffusion weighted echo planar imaging. The routine was verified by analysing the images that it had processed and was considered to create reliable images. Future studies within the field should focus on developing atlases of rats and continue the work with identifying how software developed for images of human can be applied to images of rats. / Biologer och läkare studerar komplexa biologiska processer för vilket de använder avancerade bildgivande metoder. De samlar bilder som innehåller mycket information vilken måste extraheras på ett korrekt sätt. Detta kräver god datorvana och kunskaper inom bildprocessning, vilket de sällan har. För att komma runt problemet, syftade den här masteruppsattsen till att utveckla en rutin för artefaktkorrigering och informationsextrahering från bilder tagna i ett forskningsprojekt vid Karolinska Institutet i Stockholm. Genom att utveckla rutinen, visar uppsattsen hur mjukvaror utvecklade för bilder av människa kan appliceras på bilder av råtta. Rutinen hanterar formatteringsproblem och artefaktkorrigering, beräknar diffusionsmått, och utför statistiska tester på spatiellt matchade magnetresonansavbildningar tagna med diffusionsviktade ekoplana metoder. Rutinen verifierades genom att analysera bilder som den processat och det konstaterades att den skapar korrekta bilder. Framtida studier inom området bör fokusera på att utveckla atlaser av råttor och fortsätta identifieringen av hur mjukvaror utvecklade för bilder av människa kan appliceras på bilder av råtta.

Biologists and physicians study complex biologic phenomena in which they use advanced imaging methods. They acquire images containing a lot of information which must be extracted in a correct way. This requires computer skills and knowledge in image processing methods which they seldom have. To overcome the problem, this master thesis aimed to develop a routine for artefact correction and information extraction from images acquired in a research project at the Karolinska Institutet in Stockholm. By developing the routine, the thesis showed how software developed for images of human can be applied to images of rats. The routine handles formatting issues and artefact corrections, calculates diffusion metrics, and performs statistical tests on spatially aligned magnetic resonance images of rats acquired with diffusion weighted echo planar imaging. The routine was verified by analysing the images that it had processed and was considered to create reliable images. Future studies within the field should focus on developing atlases of rats and continue the work with identifying how software developed for images of human can be applied to images of rats. / Biologer och läkare studerar komplexa biologiska processer för vilket de använder avancerade bildgivande metoder. De samlar bilder som innehåller mycket information vilken måste extraheras på ett korrekt sätt. Detta kräver god datorvana och kunskaper inom bildprocessning, vilket de sällan har. För att komma runt problemet, syftade den här masteruppsattsen till att utveckla en rutin för artefaktkorrigering och informationsextrahering från bilder tagna i ett forskningsprojekt vid Karolinska Institutet i Stockholm. Genom att utveckla rutinen, visar uppsattsen hur mjukvaror utvecklade för bilder av människa kan appliceras på bilder av råtta. Rutinen hanterar formatteringsproblem och artefaktkorrigering, beräknar diffusionsmått, och utför statistiska tester på spatiellt matchade magnetresonansavbildningar tagna med diffusionsviktade ekoplana metoder. Rutinen verifierades genom att analysera bilder som den processat och det konstaterades att den skapar korrekta bilder. Framtida studier inom området bör fokusera på att utveckla atlaser av råttor och fortsätta identifieringen av hur mjukvaror utvecklade för bilder av människa kan appliceras på bilder av råtta.

O objetivo deste trabalho é o desenvolvimento e implementação de metodologias de imagens por Ressonância Magnética Nuclear, para diminuição do tempo de aquisição, já que nos exames clínicos convencionais esse tempo é muito superior ao utilizado nessas seqüências, que é da ordem de T_ 2 , essas seqüências são baseadas na varredura única do espaço-k, convencionalmente denominada Echo Planar Imaging. Os propósitos de utilização dessa metodologia compreendem desde exames clínicos convencionais, em que se pretende analisar, em projetos futuros, eventos não periódicos de curta duração e a dinâmica dos sistemas biológicos estudados, até imagens de cavidades utilizando gases hiperpolarizados. As técnicas implementadas em comparação com as inicialmente propostas por Masfield apresentam uma diferença que é a inexistência do pulso de RF de inversão e, com isso, o tempo de duração das seqüências implementadas é ainda menor. Apenas não se deve esperar muito da qualidade das imagens sem o pós-processamento, uma vez que esse trabalho já está em andamento. / The objective of this work is the development and implementation of methodologies of images for Nuclear Magnetic Resonance, for reduction of the time of acquisition, since in the conventional clinical examinations this time is very superior to the used one in these sequences, that are of the order of T_ 2 , these sequences is based on the only sweepings of the space-k, conventionally called Echo Planar Imaging. The intentions of use of this methodology understand since conventional clinical examinations, where if it intends to analyze, in future projects, not periodic events of short duration and the dynamics of the biological systems studied, until socket images using hiperpolarizados gases. The techniques implemented in comparison with initially the proposals for Masfield present a difference that is the inexistence of the pulse of RF of inversion and, with this, the time of duration of the implemented sequences are still lesser. But if it does not have to wait very of the quality of the images without the after-processing, a time that this work already is in progress.

O objetivo deste trabalho é o desenvolvimento e implementação de metodologias de imagens por Ressonância Magnética Nuclear, para diminuição do tempo de aquisição, já que nos exames clínicos convencionais esse tempo é muito superior ao utilizado nessas seqüências, que é da ordem de T_ 2 , essas seqüências são baseadas na varredura única do espaço-k, convencionalmente denominada Echo Planar Imaging. Os propósitos de utilização dessa metodologia compreendem desde exames clínicos convencionais, em que se pretende analisar, em projetos futuros, eventos não periódicos de curta duração e a dinâmica dos sistemas biológicos estudados, até imagens de cavidades utilizando gases hiperpolarizados. As técnicas implementadas em comparação com as inicialmente propostas por Masfield apresentam uma diferença que é a inexistência do pulso de RF de inversão e, com isso, o tempo de duração das seqüências implementadas é ainda menor. Apenas não se deve esperar muito da qualidade das imagens sem o pós-processamento, uma vez que esse trabalho já está em andamento. / The objective of this work is the development and implementation of methodologies of images for Nuclear Magnetic Resonance, for reduction of the time of acquisition, since in the conventional clinical examinations this time is very superior to the used one in these sequences, that are of the order of T_ 2 , these sequences is based on the only sweepings of the space-k, conventionally called Echo Planar Imaging. The intentions of use of this methodology understand since conventional clinical examinations, where if it intends to analyze, in future projects, not periodic events of short duration and the dynamics of the biological systems studied, until socket images using hiperpolarizados gases. The techniques implemented in comparison with initially the proposals for Masfield present a difference that is the inexistence of the pulse of RF of inversion and, with this, the time of duration of the implemented sequences are still lesser. But if it does not have to wait very of the quality of the images without the after-processing, a time that this work already is in progress.

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