RubiX: combining spatial resolutions for Bayesian inference of crossing fibers in diffusion MRI

The trade-off between signal-to-noise ratio (SNR) and spatial specificity governs the choice of spatial resolution in magnetic resonance imaging (MRI); diffusion-weighted (DW) MRI is no exception. Images of lower resolution have higher signal to noise ratio, but also more partial volume artifacts. We present a data-fusion approach for tackling this trade-off by combining DW MRI data acquired both at high and low spatial resolution. We combine all data into a single Bayesian model to estimate the underlying fiber patterns and diffusion parameters. The proposed model, therefore, combines the benefits of each acquisition. We show that fiber crossings at the highest spatial resolution can be inferred more robustly and accurately using such a model compared to a simpler model that operates only on high-resolution data, when both approaches are matched for acquisition time

Advanced Algorithms for 3D Medical Image Data Fusion in Specific Medical Problems

Fúze obrazu je dnes jednou z nejběžnějších avšak stále velmi diskutovanou oblastí v lékařském zobrazování a hraje důležitou roli ve všech oblastech lékařské péče jako je diagnóza, léčba a chirurgie. V této dizertační práci jsou představeny tři projekty, které jsou velmi úzce spojeny s oblastí fúze medicínských dat. První projekt pojednává o 3D CT subtrakční angiografii dolních končetin. V práci je využito kombinace kontrastních a nekontrastních dat pro získání kompletního cévního stromu. Druhý projekt se zabývá fúzí DTI a T1 váhovaných MRI dat mozku. Cílem tohoto projektu je zkombinovat stukturální a funkční informace, které umožňují zlepšit znalosti konektivity v mozkové tkáni. Třetí projekt se zabývá metastázemi v CT časových datech páteře. Tento projekt je zaměřen na studium vývoje metastáz uvnitř obratlů ve fúzované časové řadě snímků. Tato dizertační práce představuje novou metodologii pro klasifikaci těchto metastáz. Všechny projekty zmíněné v této dizertační práci byly řešeny v rámci pracovní skupiny zabývající se analýzou lékařských dat, kterou vedl pan Prof. Jiří Jan. Tato dizertační práce obsahuje registrační část prvního a klasifikační část třetího projektu. Druhý projekt je představen kompletně. Další část prvního a třetího projektu, obsahující specifické předzpracování dat, jsou obsaženy v disertační práci mého kolegy Ing. Romana Petera.Image fusion is one of today´s most common and still challenging tasks in medical imaging and it plays crucial role in all areas of medical care such as diagnosis, treatment and surgery. Three projects crucially dependent on image fusion are introduced in this thesis. The first project deals with the 3D CT subtraction angiography of lower limbs. It combines pre-contrast and contrast enhanced data to extract the blood vessel tree. The second project fuses the DTI and T1-weighted MRI brain data. The aim of this project is to combine the brain structural and functional information that purvey improved knowledge about intrinsic brain connectivity. The third project deals with the time series of CT spine data where the metastases occur. In this project the progression of metastases within the vertebrae is studied based on fusion of the successive elements of the image series. This thesis introduces new methodology of classifying metastatic tissue. All the projects mentioned in this thesis have been solved by the medical image analysis group led by Prof. Jiří Jan. This dissertation concerns primarily the registration part of the first project and the classification part of the third project. The second project is described completely. The other parts of the first and third project, including the specific preprocessing of the data, are introduced in detail in the dissertation thesis of my colleague Roman Peter, M.Sc.

A review on a deep learning perspective in brain cancer classification

AWorld Health Organization (WHO) Feb 2018 report has recently shown that mortality rate due to brain or central nervous system (CNS) cancer is the highest in the Asian continent. It is of critical importance that cancer be detected earlier so that many of these lives can be saved. Cancer grading is an important aspect for targeted therapy. As cancer diagnosis is highly invasive, time consuming and expensive, there is an immediate requirement to develop a non-invasive, cost-effective and efficient tools for brain cancer characterization and grade estimation. Brain scans using magnetic resonance imaging (MRI), computed tomography (CT), as well as other imaging modalities, are fast and safer methods for tumor detection. In this paper, we tried to summarize the pathophysiology of brain cancer, imaging modalities of brain cancer and automatic computer assisted methods for brain cancer characterization in a machine and deep learning paradigm. Another objective of this paper is to find the current issues in existing engineering methods and also project a future paradigm. Further, we have highlighted the relationship between brain cancer and other brain disorders like stroke, Alzheimer’s, Parkinson’s, andWilson’s disease, leukoriaosis, and other neurological disorders in the context of machine learning and the deep learning paradigm

Unsupervised Retinal Blood Vessel Segmentation Technique using pdAPSO and Difference Image Methods for Detection of Diabetic Retinopathy

Retinal vessel segmentation is a practice that has the potential of enhancing accuracy in the diagnosis and timely prevention of illnesses that are related to blood vessels. Acute damage to the retinal vessel has been identified to be the main cause of blindness and impaired vision. A timely detection and control of these illnesses can greatly decrease the number of loss of sight cases. However, the manual protocol for such detection is laborious and although autonomous methods have been recommended, the accuracy of these methods is often unreliable. We propose the utilization of the Primal-Dual Asynchronous Particle Swarm Optimisation (pdAPSO) and differential image methods in addressing the drawbacks associated with segmentation of retinal vessels in this study. The fusion of pdAPSO and differential image (which focuses on the median filter) produced a significant enhancement in the segmentation of huge and miniscule retinal vessels. In addition, the method also decreased erroneous detection near the edge of the retinal (that is not sensitive to light). The results are favourable for the median filter when compared to mean filter and Gaussian filter. The accuracy rate of 0.9559 (with a specificity of sensitivity rate of 0.9855), and a sensitivity rate of 0.7218 were obtained when tested using the Digital Retinal Images for Vessel Extraction database. The above result is a pointer that our approach will help in detecting and diagnosing the damage done to the retinal and thereby preventing loss of sight

Automated detection of brain abnormalities in neonatal hypoxia ischemic injury from MR images.

We compared the efficacy of three automated brain injury detection methods, namely symmetry-integrated region growing (SIRG), hierarchical region splitting (HRS) and modified watershed segmentation (MWS) in human and animal magnetic resonance imaging (MRI) datasets for the detection of hypoxic ischemic injuries (HIIs). Diffusion weighted imaging (DWI, 1.5T) data from neonatal arterial ischemic stroke (AIS) patients, as well as T2-weighted imaging (T2WI, 11.7T, 4.7T) at seven different time-points (1, 4, 7, 10, 17, 24 and 31 days post HII) in rat-pup model of hypoxic ischemic injury were used to assess the temporal efficacy of our computational approaches. Sensitivity, specificity, and similarity were used as performance metrics based on manual ('gold standard') injury detection to quantify comparisons. When compared to the manual gold standard, automated injury location results from SIRG performed the best in 62% of the data, while 29% for HRS and 9% for MWS. Injury severity detection revealed that SIRG performed the best in 67% cases while 33% for HRS. Prior information is required by HRS and MWS, but not by SIRG. However, SIRG is sensitive to parameter-tuning, while HRS and MWS are not. Among these methods, SIRG performs the best in detecting lesion volumes; HRS is the most robust, while MWS lags behind in both respects

A Bayesian Abduction Model For Sensemaking

This research develops a Bayesian Abduction Model for Sensemaking Support (BAMSS) for information fusion in sensemaking tasks. Two methods are investigated. The first is the classical Bayesian information fusion with belief updating (using Bayesian clustering algorithm) and abductive inference. The second method uses a Genetic Algorithm (BAMSS-GA) to search for the k-best most probable explanation (MPE) in the network. Using various data from recent Iraq and Afghanistan conflicts, experimental simulations were conducted to compare the methods using posterior probability values which can be used to give insightful information for prospective sensemaking. The inference results demonstrate the utility of BAMSS as a computational model for sensemaking. The major results obtained are: (1) The inference results from BAMSS-GA gave average posterior probabilities that were 103 better than those produced by BAMSS; (2) BAMSS-GA gave more consistent posterior probabilities as measured by variances; and (3) BAMSS was able to give an MPE while BAMSS-GA was able to identify the optimal values for kMPEs. In the experiments, out of 20 MPEs generated by BAMSS, BAMSS-GA was able to identify 7 plausible network solutions resulting in less amount of information needed for sensemaking and reducing the inference search space by 7/20 (35%). The results reveal that GA can be used successfully in Bayesian information fusion as a search technique to identify those significant posterior probabilities useful for sensemaking. BAMSS-GA was also more robust in overcoming the problem of bounded search that is a constraint to Bayesian clustering and inference state space in BAMSS