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Comparing the Training Performance of a Deep Neural Network for Accelerated MRI Reconstruction Using Synthesized and Realistic k-Space Data
Get PDFMagnetic Resonance Imaging (MRI) is a powerful medical imaging modality used as a diagnostic tool. There is a steady rise in the imagining examination. Trends from 2000 - 2016 showed that nearly 16 million to 21 million patients had enrolled annually in various US health care systems. The number of MRIs per 1000 increased from 62 per 1000 to 139 per 1000 patients from 2000 to 2016. MR images are usually stored in Picture Archiving and Communication Systems (PACS) in Digital Imaging and Communication in Medicine (DICOM). DICOM format includes a header and imaging data. MRI k-space is the raw data obtained during the MR signal acquisition. The file size of complex MR data is huge. It is generally transformed into the anatomical imaging data, and raw data is discarded and not transferred to the PACS. The abundant DICOM data has the potential to be used for training neural networks. Deep Neural Network models depend on the extensive training datasets. DICOM images are magnitude images without the image phase. It is essential to understand the effect of missing image phase information to use the DICOM data for this training task effectively. My thesis attempts to compare a deep neural network's performance for accelerated MRI reconstruction using the k-space to DICOM only data. MR imaging offers a great deal of control to the user to acquire the data and reconstruct the clinical images. All this comes at the cost of an increase in the acquisition time. Typical scan times are between 30 to 40 mins. Scan times go up to 60 mins if a contrast agent needs to be administered. Such long acquisition times are not only expensive but a cause of inconvenience to the subject as it is impossible to stay motionless in the bore during the whole duration. Two areas are of interest to reduce the scan time, (i) accelerated acquisition and (ii) fast and efficient reconstruction. Methods like compressed sensing and parallel imaging are used to accelerate MRI acquisition. Compressed sensing achieves scan acceleration by overcoming the requirement of Nyquist sampling criteria. An undersampling pattern like the Poisson Disk undersampling pattern is used to acquire an incoherent random sparse signal instead of the full k-space. The "sigpy.mri" python library's "Poisson" API was used to simulate this undersampling. This Python API generates a variable-density Poisson-disc sampling pattern. Compressed Sensing theory mentions that image reconstruction would be possible using signals less than the number indicated by Nyquist as long as the k-space undersampling is done incoherently, which does not lead to structural aliasing when the anatomical image is constructed. This algorithm combines the undersampling with partial Fourier imaging. This API uses a fully sampled calibration region at the center of the k-space in addition to the acceleration factor. The acceleration factor is used for undersampling the region outside the fully sampled center region. Poisson disk undersampling does random sampling while constraining the maximum and minimum distance. This scheme leads to incoherent sampling and avoids structural artifacts. After the image acquisition comes, the reconstruction of the fully sampled k-space or the anatomical image with good SNR. A deep-learning neural network was trained to perform the reconstruction of the retrospectively undersampled data. The undersampled raw k-space data's training performance is compared with that of the undersampled k-space data obtained from the DICOM data. Our experiments have shown that the magnitude obtained from raw k-space data has consistently shown better initial training performance and faster convergence when compared to the magnitude image obtained from the DICOM image. It is also observed that after training enough epochs, the performance of the model trained using raw data is comparable to that of the DICOM images. The significance of this finding is in the fact that the abundantly available DICOM data can be used to train a deep neural network to perform reconstruction of the undersampled k-space. FastMRI is a research project from Facebook AI(FAIR) and NYU Langone Health. The dataset for this project is publicly available. This dataset has two types of scans, knee MRI and brain MRI. For this work, we have used single coil knee MRI data. For performing the training, 2D slices from these images are used from the training dataset's single-coil knee MRI volumes. The training dataset has 973 volumes and a total of 34,742 slices
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
Author Under Sail The Imagination of Jack London, 1893-1902
No full textIn Author Under Sail, Jay Williams offers the first complete literary biography of Jack London as a professional writer engaged in the labor of writing. It examines the authorial imagination in London's work, the use of imagination in both his fiction and nonfiction, and the ways he defined imagination in the creative process in his business dealings with his publishers, editors, and agents. In this first volume of a two-volume biography, Williams traverses the years 1893 to 1902, from London's "Story of a Typhoon" to The People of the Abyss. The Jack London who emerges in the pages of Author Under Sail is a writer whose partnership with publishers, most notably his productive alliance with George Brett of Macmillan, was one of the most formative in American literary history. London pioneered many author models during the heyday of realism and naturalism, blurring the boundaries of these popular genres by focusing on absorption and theatricality and the representation of the seen and unseen. London created an impassioned, sincere, and extremely personal realism unlike that of other American writers of the time. Author Under Sail is a literary tour de force that reveals the full range of London as writer, creative citizen, and entrepreneur at the same time it sheds light on the maverick side of machine-age literature.Intro -- Title Page -- Copyright Page -- Dedication -- Contents -- Acknowledgments -- Introduction -- 1. Spirit Truth -- 2. From Absorption to Theatricality and Back Again -- 3. "I Will Build a New Present" -- 4. Sons as Authors -- 5. Fathers as Publishers -- 6. The Daughter as Author -- 7. Lovers as Authors -- 8. At Sea with the Family -- 9. Yellow News, Yellow Stories -- 10. The Return Home -- Notes -- Bibliography -- Index -- About Jay WilliamsIn Author Under Sail, Jay Williams offers the first complete literary biography of Jack London as a professional writer engaged in the labor of writing. It examines the authorial imagination in London's work, the use of imagination in both his fiction and nonfiction, and the ways he defined imagination in the creative process in his business dealings with his publishers, editors, and agents. In this first volume of a two-volume biography, Williams traverses the years 1893 to 1902, from London's "Story of a Typhoon" to The People of the Abyss. The Jack London who emerges in the pages of Author Under Sail is a writer whose partnership with publishers, most notably his productive alliance with George Brett of Macmillan, was one of the most formative in American literary history. London pioneered many author models during the heyday of realism and naturalism, blurring the boundaries of these popular genres by focusing on absorption and theatricality and the representation of the seen and unseen. London created an impassioned, sincere, and extremely personal realism unlike that of other American writers of the time. Author Under Sail is a literary tour de force that reveals the full range of London as writer, creative citizen, and entrepreneur at the same time it sheds light on the maverick side of machine-age literature.Description based on publisher supplied metadata and other sources.Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, YYYY. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries
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