A Survey of DICOM Viewer Software to Integrate Clinical Research and Medical Imaging

Haak, Daniel; Page, Charles-E.; Deserno, Thomas M.

doi:10.1007/s10278-015-9833-1

Cited by 58 publications

(31 citation statements)

References 22 publications

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“…It supports over thirty file formats commonly used in medical imaging, including DICOM and NIfTI, and more than ten 3D surface mesh formats. [13] It also supports multi-scale and multi-dimensional image research from microscopy, to CT, PET, and MRI. BRICS's inclusion of the MIPAV tool gives powerful capabilities for uploading image packages, as well as image analysis, not found in other informatics systems.…”

Section: Figure 2amentioning

confidence: 93%

Standardized Informatics Computing Platform for Advancing Biomedical Discovery Through Data Sharing

Navale

McCreedy³

et al. 2018

Preprint

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Objective: The goal is to develop a standardized informatics computing system that can support end-to-end research data lifecycle management for biomedical research applications. Materials and Methods:Design and implementation of biomedical research informatics computing system (BRICS) is demonstrated. The system architecture is modular in design with several integrated tools: global unique identifier, validation, upload, download and query tools that support user friendly informatics system capability.

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Section: Figure 2amentioning

confidence: 93%

Standardized Informatics Computing Platform for Advancing Biomedical Discovery Through Data Sharing

Navale

McCreedy³

et al. 2018

Preprint

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“…The open-source software MIPAV version 5.4.4 – Medical Image Processing, Analysis and Visualization; Center for Information Technology, National Institutes of Health ( http://www.mipav.cit.nih.gov ) – was used for the development and validation of the multipurpose CT window. [ 4 ]…”

Section: Methodsmentioning

confidence: 99%

Multipurpose computed tomography window for fusion display with functional imaging

Nguyen

Vejdani

2018

World J Nucl Med

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Current positron emission tomography/computed tomography (PET/CT) and single photon emission CT (SPECT)/CT displays have major drawbacks, in that the CT only shows one tissue type at a time, which leads to a suboptimal fusion display. We developed a multipurpose CT level/window aiming at enhancing fusion display. A total of thirty CT examinations as part of fluorodeoxyglucose PET/CT examinations (15 were open source from the OsiriX website and 15 from our PET facility) and the open-source software MIPAV were used. During the development phase, a nuclear medicine physician manually modified the lookup table in a way that preserved the soft tissue contrast as well as enhanced the lung and bone tissue as much as possible. The developed multipurpose CT window was used in the subsequent validation phase and scored by two nuclear medicine physicians, who scored the image quality based on a 3-point score. Descriptive statistics was used to summarize the visual scores. The multipurpose CT window is a composite of several segments of linear CT levels/windows and contains an inverted linear level/window in the low range of Hounsfield unit designed to enhance lung/soft tissue contrast. In doing so, the multipurpose CT window preserves the high soft tissue contrast; the visualization of the lung parenchyma is satisfactory; the contrast for the bone tissue is improved but remains suboptimal when compared with conventional bone window. The multipurpose CT window was found to be “very useful” (median score 3; 95% confidence interval [CI] 2.0–3.0) for the purpose of fusion with functional imaging, with a prevalence asymmetry index 0.97 (95% CI 0.83–1.0). The multipurpose CT window was developed for image fusion and is not intended for diagnostic purposes. It shows favorable similarities to conventional CT windows with only minor artifacts and allows for enhanced visualization of fused PET/CT and SPECT/CT images. The multipurpose CT window is particularly valuable for case review/demonstrations on standard personal computers and handheld devices (smartphones, tablets).

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“…Several arguments exist for the conversion of probabilistic tractography into this format. For example, overlaying images with raw streamline files or non-binary voxelwise representations thereof is not well supported by Picture Archiving and Communications System (PACS) oriented DICOM viewers that are central to clinical workflows (9,10). Clinicians are also generally more familiar with the more simplistic visualisations from deterministic diffusion tensor tractography that historically have dominated tractography research in surgical journals (for a review, see (11)).…”

Section: Introductionmentioning

confidence: 99%

How Many Streamlines are Required for Reliable Probabilistic Tractography? Solutions for Microstructural Measurements and Neurosurgical Planning

Reid

Cespedes

Pannek

2020

Preprint

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16Diffusion MRI tractography is commonly used to delineate white matter tracts. These delineations can 17 be used for planning neurosurgery or for identifying regions of interest from which microstructural 18 measurements can be taken. Probabilistic tractography produces different delineations each time it 19 is run, potentially leading to microstructural measurements or anatomical delineations that are not 20 reproducible. Generating a sufficiently large number of streamlines is required to avoid this scenario, 21 but what constitutes "sufficient" is difficult to assess and so streamline counts are typically chosen in 22 an arbitrary or qualitative manner. This work explores several factors influencing tractography 23 reliability and details two methods for estimating this reliability. The first method automatically 24 estimates the number of streamlines required to achieve reliable microstructural measurements, 25 whilst the second estimates the number of streamlines required to achieve a reliable binarised 26 trackmap than can be used clinically. Using these methods, we calculated the number of streamlines 27 required to achieve a range of quantitative reproducibility criteria for three anatomical tracts in 40 28Human Connectome Project datasets. Actual reproducibility was checked by repeatedly generating 29 the tractograms with the calculated numbers of streamlines. We found that the required number of 30 streamlines varied strongly by anatomical tract, image resolution, number of diffusion directions, the 31 degree of reliability desired, the microstructural measurement of interest, and/or the specifics on how 32 the tractogram was converted to a binary volume. The proposed methods consistently predicted 33 streamline counts that achieved the target reproducibility. Implementations are made available to 34 enable the scientific community to more-easily achieve reproducible tractography. 35 Keywords 36 diffusion weighted imaging; diffusion tractography; power analysis; streamline count; bootstrapping; 37 reproducibility. 38 39 40 3

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A Survey of DICOM Viewer Software to Integrate Clinical Research and Medical Imaging

Cited by 58 publications

References 22 publications

Standardized Informatics Computing Platform for Advancing Biomedical Discovery Through Data Sharing

Standardized Informatics Computing Platform for Advancing Biomedical Discovery Through Data Sharing

Multipurpose computed tomography window for fusion display with functional imaging

How Many Streamlines are Required for Reliable Probabilistic Tractography? Solutions for Microstructural Measurements and Neurosurgical Planning

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