The cohort size required in epidemiological imaging genetics studies often mandates the pooling of data from multiple hospitals. Patient data, however, is subject to strict privacy protection regimes, and physical data storage may be legally restricted to a hospital network. To enable biomarker discovery, fast data access and interactive data exploration must be combined with high-performance computing resources, while respecting privacy regulations. We present a system using fast and inherently secure light-paths to access distributed data, thereby obviating the need for a central data repository. A secure private cloud computing framework facilitates interactive, computationally intensive exploration of this geographically distributed, privacy sensitive data. As a proof of concept, MRI brain imaging data hosted at two remote sites were processed in response to a user command at a third site. The system was able to automatically start virtual machines, run a selected processing pipeline and write results to a user accessible database, while keeping data locally stored in the hospitals. Individual tasks took approximately 50% longer compared to a locally hosted blade server but the cloud infrastructure reduced the total elapsed time by a factor of 40 using 70 virtual machines in the cloud. We demonstrated that the combination light-path and private cloud is a viable means of building an analysis infrastructure for secure data analysis. The system requires further work in the areas of error handling, load balancing and secure support of multiple users.
It is still unclear whether periventricular and subcortical white matter lesions (WMLs) differ in etiology or clinical
consequences. Studies addressing this issue would benefit from automated segmentation and localization
of WMLs. Several papers have been published on WML segmentation in MR images. Automated localization
however, has not been investigated as much. This work presents and evaluates a novel method to label segmented
WMLs as periventricular and subcortical.
The proposed technique combines tissue classification and registration-based segmentation to outline the ventricles
in MRI brain data. The segmented lesions can then be labeled into periventricular WMLs and subcortical
WMLs by applying region growing and morphological operations.
The technique was tested on scans of 20 elderly subjects in which neuro-anatomy experts manually segmented
WMLs. Localization accuracy was evaluated by comparing the results of the automated method with a manual
localization. Similarity indices and volumetric intraclass correlations between the automated and the manual
localization were 0.89 and 0.95 for periventricular WMLs and 0.64 and 0.89 for subcortical WMLs, respectively.
We conclude that this automated method for WML localization performs well to excellent in comparison to the
gold standard.
Conventional k-Nearest-Neighbor (kNN) classification, which has been successfully applied to classify brain tissue, requires laborious training on manually labeled subjects. In this work, the performance of kNN-based segmentation of gray matter (GM), white matter (WM) and cerebrospinal fluid (CSF) using manual training is compared with a new method, in which training is automated using an atlas. From 12 subjects, standard T2 and PD scans and a high-resolution, high-contrast scan (Siemens T1-weighted HASTE sequence with reverse contrast) were used as feature sets. For the conventional kNN method, manual segmentations were used for training, and classifications were evaluated in a leave-one-out study. The performance as a function of the number of samples per tissue, and k was studied. For fully automated training, scans were registered to a probabilistic brain atlas. Initial training samples were randomly selected per tissue based on a threshold on the tissue probability. These initials were processed to keep the most reliable samples. Performance of the method for varying the threshold on the tissue probability method was studied. By measuring the percentage overlap (SI), classification results of both methods were validated. For conventional kNN classification, varying the number of training samples did not result in significant differences, while increasing k gave significantly better results. In the method using automated training, there is an overestimation of GM at the expense of CSF at higher thresholds on the tissue probability maps. The difference between the conventional method (k=45) and the observers was not significantly larger than inter-observer variability for all tissue types. The automated method performed slightly worse and performed equal to the observers for WM, and less for CSF and GM. From these results it can be concluded that conventional kNN classification may replace manual segmentation, and that atlas-based kNN segmentation has strong potential for fully automated segmentation, without the need of laborious manual training.
Imaging of small high-density structures, such as calcifications, with computed tomography (CT) is limited by the spatial resolution of the system. Blur causes small calcifications to be imaged with lower contrast and overestimated volume, thereby hampering the analysis of vessels. The aim of this work is to reduce the blur of calcifications by applying three-dimensional (3D) deconvolution. Unfortunately, the high-frequency amplification of the deconvolution produces edge-related ring artifacts and enhances noise and original artifacts, which degrades the imaging of low-density structures. A method, referred to as Histogram-based Selective Deblurring (HiSD), was implemented to avoid these negative effects. HiSD uses the histogram information to generate a restored image in which the low-intensity voxel information of the observed image is combined with the high-intensity voxel information of the deconvolved image. To evaluate HiSD we scanned four in-vitro atherosclerotic plaques of carotid arteries with a multislice spiral CT and with a microfocus CT (μCT), used as reference. Restored images were generated from the observed images, and qualitatively and quantitatively compared with their corresponding μCT images. Transverse views and maximum-intensity projections of restored images show the decrease of blur of the calcifications in 3D. Measurements of the areas of 27 calcifications and total volumes of calcification of 4 plaques show that the overestimation of calcification was smaller for restored images (mean-error: 90% for area; 92% for volume) than for observed images (143%; 213%, respectively). The qualitative and quantitative analyses show that the imaging of calcifications in CT can be improved considerably by applying HiSD.
Magnetic Resonance Thermometry imaging is a non-invasive method for temperature monitoring in hyperthermia treatment. The temperature can be determined from the phase shift in a gradient-echo sequence. Due to large temperature variations, the phase shift may exceed the (-π ,π) radians interval. The phase value beyond this interval will be wrapped. Unfortunately, the temperature is only proportional to the absolute phase change. Therefore, phase unwrapping (PU) is required to recover the absolute phase from the wrapped representation. While the phase may contain spurious discontinuities, the algorithm must distinguish them from true phase discontinuities. We propose additional processing to support PU in order to improve the algorithm for recovery of the best estimation of absolute phase. The Minimum Weight Discontinuity (MWD) algorithm was used for PU. The steps to be taken on additional processing consist of applying a Gaussian filter to the raw complex MRI images, deriving the weights of a quality map, and segmenting unreliable regions using the magnitude image. The raw wrapped phase images, acquired from a phantom and from a porcine liver (acquired under laser irradiation), were used to test the effect of additional processing. The effect was compared with the conventional approach (i.e. mere unwrapping with the MWD algorithm).
Advanced multiple beam equalization radiography (Amber) has been successfully applied to chest radiography. More recently, the applications have been extended to mammography. The Amber chest unit (Oldelft, Delft, The Netherlands) controls the local X-ray exposure to the patient by means of a feedback loop consisting of a number of detectors in front of the film cassette and the same number of absorbers in front of the X-ray tube. The detector readouts and a predefined compression curve determine the position of the absorbers, while the patient is being scanned by means of a horizontally oriented fan beam. As a consequence, the multiple beam equalization technology has introduced new concepts such as beam profile, compression curve, number of absorbers, and detector weighting function to projection imaging. In order to optimize these different parameters we have developed a computer program, which simulates the multiple beam equalization techniques. Conventionally exposed films are laser scanned resulting in a matrix of optical density values. The program calculates for each pixel the X-ray transmission. These X-ray transmission values are the basis for the simulations with varying beam profile characteristics (i.e. the intensity distribution of the X-ray beam of a channel in horizontal and vertical direction), compression curves, number of channels, detector weighting functions and H&D film curves In order to accurately simulate a particular exposure, the program can be calibrated using optical density and X-ray dose measurements on a conventional X-ray unit or on the Amber unit.
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