Acceleration of Magnetic Resonance Fingerprinting Reconstruction Using Denoising and Self-Attention Pyramidal Convolutional Neural Network.

Magnetic resonance fingerprinting (MRF) based on echo-planar imaging (EPI) enables whole-brain imaging to rapidly obtain T1 and T2* relaxation time maps. Reconstructing parametric maps from the MRF scanned baselines by the inner-product method is computationally expensive. We aimed to accelerate the reconstruction of parametric maps for MRF-EPI by using a deep learning model. The proposed approach uses a two-stage model that first eliminates noise and then regresses the parametric maps. Parametric maps obtained by dictionary matching were used as a reference and compared with the prediction results of the two-stage model. MRF-EPI scans were collected from 32 subjects. The signal-to-noise ratio increased significantly after the noise removal by the denoising model. For prediction with scans in the testing dataset, the mean absolute percentage errors between the standard and the final two-stage model were 3.1%, 3.2%, and 1.9% for T1, and 2.6%, 2.3%, and 2.8% for T2* in gray matter, white matter, and lesion locations, respectively. Our proposed two-stage deep learning model can effectively remove noise and accurately reconstruct MRF-EPI parametric maps, increasing the speed of reconstruction and reducing the storage space required by dictionaries.

Multiparametric MRI in the Diagnosis of Prostate Cancer: Physical Foundations, Limitations, and Prospective Advances of Diffusion-Weighted MRI.

BACKGROUND: Diffusion-weighted imaging (DWI) is an essential component of the multiparametric MRI exam for the diagnosis and assessment of prostate cancer (PCa). Over the last two decades, various models have been developed to quantitatively correlate the DWI signal with microstructural characteristics of prostate tissue. The simplest approach (ADC: apparent diffusion coefficient) - currently established as the clinical standard - describes monoexponential decay of the DWI signal. While numerous studies have shown an inverse correlation of ADC values with the Gleason score, the ADC model lacks specificity and is based on water diffusion dynamics that are not true in human tissue. This article aims to explain the biophysical limitations of the standard DWI model and to discuss the potential of more complex, advanced DWI models. METHODS: This article is a review based on a selective literature review. RESULTS: Four phenomenological DWI models are introduced: diffusion tensor imaging, intravoxel incoherent motion, biexponential model, and diffusion kurtosis imaging. Their parameters may potentially improve PCa diagnostics but show varying degrees of statistical significance with respect to the detection and characterization of PCa in current studies. Phenomenological model parameters lack specificity, which has motivated the development of more descriptive tissue models that directly relate microstructural features to the DWI signal. Finally, we present two of such structural models, i. e. the VERDICT (Vascular, Extracellular, and Restricted Diffusion for Cytometry in Tumors) and RSI (Restriction Spectrum Imaging) model. Both have shown promising results in initial studies regarding the characterization and prognosis of PCa. CONCLUSION: Recent developments in DWI techniques promise increasing accuracy and more specific statements about microstructural changes of PCa. However, further studies are necessary to establish a standardized DWI protocol for the diagnosis of PCa. KEY POINTS: · DWI is paramount to the mpMRI exam for the diagnosis of PCa.. · Though of clinical value, the ADC model lacks specificity and oversimplifies tissue complexities.. · Advanced phenomenological and structural models have been developed to describe the DWI signal.. · Phenomenological models may improve diagnostics but show inconsistent results regarding PCa assessment.. · Structural models have demonstrated promising results in initial studies regarding PCa characterization.. CITATION FORMAT: · Wichtmann BD, Zöllner FG, Attenberger UI et al. Multiparametric MRI in the Diagnosis of Prostate Cancer: Physical Foundations, Limitations, and Prospective Advances of Diffusion-Weighted MRI. Fortschr Röntgenstr 2021; 193: 399 - 409.

Deterministic Arterial Input Function selection in DCE-MRI for automation of quantitative perfusion calculation of colorectal cancer.

Development of a deterministic algorithm for automated detection of the Arterial Input Function (AIF) in DCE-MRI of colorectal cancer. Using a filter pipeline to determine the AIF region of interest. Comparison to algorithms from literature with mean squared error and quantitative perfusion parameter Ktrans. The AIF found by our algorithm has a lower mean squared error (0.0022 ±â€¯0.0021) in reference to the manual annotation than comparable algorithms. The error of Ktrans (21.52 ±â€¯17.2%) is lower than that of other algorithms. Our algorithm generates reproducible results and thus supports a robust and comparable perfusion analysis.

Influence of Gadolinium-Based Contrast Agents on Tissue Sodium Quantification in Sodium Magnetic Resonance Imaging.

OBJECTIVES: Sodium magnetic resonance (MR) imaging provides noninvasive insights to cellular processes by measuring tissue sodium concentration (TSC). Many clinical studies combine sodium MR imaging with clinical standard MR procedures, in which contrast media is frequently administered. This work investigates the influence of gadolinium-based contrast agents on quantification of TSC. Thus, either scan pauses between early and late contrast-enhanced acquisitions can be used efficiently or sodium imaging can be performed as the final scan after dynamic contrast-enhanced acquisition. MATERIALS AND METHODS: For this study, 2 gadolinium-based contrast agents, Dotarem and Gadovist, were diluted with saline solution covering contrast agent concentrations in a clinical range. In addition, agarose-based sample series were created to simulate tissue relaxation time behavior. In vivo, the influence of Dotarem on sodium acquisition and TSC quantification was investigated in 1 ischemic stroke patient. RESULTS: Proton relaxation times decreased for increasing contrast agent concentrations as hyperbolic functions. Sodium relaxation times displayed a negative slope in regression analysis in most cases. The largest influence (-1.52 milliseconds per mmol/L contrast agent) was measured for sodium T1. Worst case calculations in ultrashort echo time sequence signal analysis showed a signal drop of (1.21% ± 0.56%) on tissue sodium quantification. In vivo sodium brain acquisitions of a stroke patient before and after Dotarem injection resulted in statistically nonsignificant differences in TSC quantification of relevant tissues and stroke areas (P > 0.05). CONCLUSIONS: Our study showed a quantitative influence of Dotarem and Gadovist on sodium relaxation times. However, quantification of TSC was not impaired, which was proven by worst case calculations and nonsignificant differences in vivo in an ischemic stroke patient. We suggest performing sodium imaging in useful clinical positions in protocols regardless of included Dotarem or Gadovist administrations. Being flexible in the study protocol design will strengthen ongoing sodium imaging investigations for various pathologies.

Identification of a characteristic vascular belt zone in human colorectal cancer.

BLOOD VESSELS IN CANCER: Intra-tumoral blood vessels are of supreme importance for tumor growth, metastasis and therapy. Yet, little is known about spatial distribution patterns of these vessels. Most experimental or theoretical tumor models implicitly assume that blood vessels are equally abundant in different parts of the tumor, which has far-reaching implications for chemotherapy and tumor metabolism. In contrast, based on histological observations, we hypothesized that blood vessels follow specific spatial distribution patterns in colorectal cancer tissue. We developed and applied a novel computational approach to identify spatial patterns of angiogenesis in histological whole-slide images of human colorectal cancer. A CHARACTERISTIC SPATIAL PATTERN OF BLOOD VESSELS IN COLORECTAL CANCER: In 33 of 34 (97%) colorectal cancer primary tumors blood vessels were significantly aggregated in a sharply limited belt-like zone at the interface of tumor tissue to the intestinal lumen. In contrast, in 11 of 11 (100%) colorectal cancer liver metastases, a similar hypervascularized zone could be found at the boundary to surrounding liver tissue. Also, in an independent validation cohort, we found this vascular belt zone: 22 of 23 (96%) samples of primary tumors and 15 of 16 (94%) samples of liver metastases exhibited the above-mentioned spatial distribution. SUMMARY AND IMPLICATIONS: We report consistent spatial patterns of tumor vascularization that may have far-reaching implications for models of drug distribution, tumor metabolism and tumor growth: luminal hypervascularization in colorectal cancer primary tumors is a previously overlooked feature of cancer tissue. In colorectal cancer liver metastases, we describe a corresponding pattern at the invasive margin. These findings add another puzzle piece to the complex concept of tumor heterogeneity.

Polyphonic sonification of electrocardiography signals for diagnosis of cardiac pathologies.

Electrocardiography (ECG) data are multidimensional temporal data with ubiquitous applications in the clinic. Conventionally, these data are presented visually. It is presently unclear to what degree data sonification (auditory display), can enable the detection of clinically relevant cardiac pathologies in ECG data. In this study, we introduce a method for polyphonic sonification of ECG data, whereby different ECG channels are simultaneously represented by sound of different pitch. We retrospectively applied this method to 12 samples from a publicly available ECG database. We and colleagues from our professional environment then analyzed these data in a blinded way. Based on these analyses, we found that the sonification technique can be intuitively understood after a short training session. On average, the correct classification rate for observers trained in cardiology was 78%, compared to 68% and 50% for observers not trained in cardiology or not trained in medicine at all, respectively. These values compare to an expected random guessing performance of 25%. Strikingly, 27% of all observers had a classification accuracy over 90%, indicating that sonification can be very successfully used by talented individuals. These findings can serve as a baseline for potential clinical applications of ECG sonification.

Color-coded visualization of magnetic resonance imaging multiparametric maps.

Multiparametric magnetic resonance imaging (mpMRI) data are emergingly used in the clinic e.g. for the diagnosis of prostate cancer. In contrast to conventional MR imaging data, multiparametric data typically include functional measurements such as diffusion and perfusion imaging sequences. Conventionally, these measurements are visualized with a one-dimensional color scale, allowing only for one-dimensional information to be encoded. Yet, human perception places visual information in a three-dimensional color space. In theory, each dimension of this space can be utilized to encode visual information. We addressed this issue and developed a new method for tri-variate color-coded visualization of mpMRI data sets. We showed the usefulness of our method in a preclinical and in a clinical setting: In imaging data of a rat model of acute kidney injury, the method yielded characteristic visual patterns. In a clinical data set of N = 13 prostate cancer mpMRI data, we assessed diagnostic performance in a blinded study with N = 5 observers. Compared to conventional radiological evaluation, color-coded visualization was comparable in terms of positive and negative predictive values. Thus, we showed that human observers can successfully make use of the novel method. This method can be broadly applied to visualize different types of multivariate MRI data.

Multi-class texture analysis in colorectal cancer histology.

Automatic recognition of different tissue types in histological images is an essential part in the digital pathology toolbox. Texture analysis is commonly used to address this problem; mainly in the context of estimating the tumour/stroma ratio on histological samples. However, although histological images typically contain more than two tissue types, only few studies have addressed the multi-class problem. For colorectal cancer, one of the most prevalent tumour types, there are in fact no published results on multiclass texture separation. In this paper we present a new dataset of 5,000 histological images of human colorectal cancer including eight different types of tissue. We used this set to assess the classification performance of a wide range of texture descriptors and classifiers. As a result, we found an optimal classification strategy that markedly outperformed traditional methods, improving the state of the art for tumour-stroma separation from 96.9% to 98.6% accuracy and setting a new standard for multiclass tissue separation (87.4% accuracy for eight classes). We make our dataset of histological images publicly available under a Creative Commons license and encourage other researchers to use it as a benchmark for their studies.

New Colors for Histology: Optimized Bivariate Color Maps Increase Perceptual Contrast in Histological Images.

BACKGROUND: Accurate evaluation of immunostained histological images is required for reproducible research in many different areas and forms the basis of many clinical decisions. The quality and efficiency of histopathological evaluation is limited by the information content of a histological image, which is primarily encoded as perceivable contrast differences between objects in the image. However, the colors of chromogen and counterstain used for histological samples are not always optimally distinguishable, even under optimal conditions. METHODS AND RESULTS: In this study, we present a method to extract the bivariate color map inherent in a given histological image and to retrospectively optimize this color map. We use a novel, unsupervised approach based on color deconvolution and principal component analysis to show that the commonly used blue and brown color hues in Hematoxylin-3,3'-Diaminobenzidine (DAB) images are poorly suited for human observers. We then demonstrate that it is possible to construct improved color maps according to objective criteria and that these color maps can be used to digitally re-stain histological images. VALIDATION: To validate whether this procedure improves distinguishability of objects and background in histological images, we re-stain phantom images and N = 596 large histological images of immunostained samples of human solid tumors. We show that perceptual contrast is improved by a factor of 2.56 in phantom images and up to a factor of 2.17 in sets of histological tumor images. CONTEXT: Thus, we provide an objective and reliable approach to measure object distinguishability in a given histological image and to maximize visual information available to a human observer. This method could easily be incorporated in digital pathology image viewing systems to improve accuracy and efficiency in research and diagnostics.

Continuous representation of tumor microvessel density and detection of angiogenic hotspots in histological whole-slide images.

Blood vessels in solid tumors are not randomly distributed, but are clustered in angiogenic hotspots. Tumor microvessel density (MVD) within these hotspots correlates with patient survival and is widely used both in diagnostic routine and in clinical trials. Still, these hotspots are usually subjectively defined. There is no unbiased, continuous and explicit representation of tumor vessel distribution in histological whole slide images. This shortcoming distorts angiogenesis measurements and may account for ambiguous results in the literature. In the present study, we describe and evaluate a new method that eliminates this bias and makes angiogenesis quantification more objective and more efficient. Our approach involves automatic slide scanning, automatic image analysis and spatial statistical analysis. By comparing a continuous MVD function of the actual sample to random point patterns, we introduce an objective criterion for hotspot detection: An angiogenic hotspot is defined as a clustering of blood vessels that is very unlikely to occur randomly. We evaluate the proposed method in N=11 images of human colorectal carcinoma samples and compare the results to a blinded human observer. For the first time, we demonstrate the existence of statistically significant hotspots in tumor images and provide a tool to accurately detect these hotspots.

Blood flow quantification from 2D phase contrast MRI in renal arteries using an unsupervised data driven approach.

We present a clustering approach to segment the renal artery from 2D PC Cine MR images to measure arterial blood velocity and flow. Such information is important in grading renal artery stenosis and to support the decision on surgical interventions like percutaneous transluminal angioplasty. Results from 20 data sets (3 volunteers, 7 patients) show that the renal arteries could be extracted automatically and the corresponding velocity profiles were close (r = 0.977) to that obtained by manual delineations of the vessel areas.