ROCKETSHIP: a flexible and modular software tool for the planning, processing and analysis of dynamic MRI studies

Background: Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is a promising technique to characterize pathology and evaluate treatment response. However, analysis of DCE-MRI data is complex and benefits from concurrent analysis of multiple kinetic models and parameters. Few software tools are currently available that specifically focuses on DCE-MRI analysis with multiple kinetic models. Here, we developed ROCKETSHIP, an open-source, flexible and modular software for DCE-MRI analysis. ROCKETSHIP incorporates analyses with multiple kinetic models, including data-driven nested model analysis. Results: ROCKETSHIP was implemented using the MATLAB programming language. Robustness of the software to provide reliable fits using multiple kinetic models is demonstrated using simulated data. Simulations also demonstrate the utility of the data-driven nested model analysis. Applicability of ROCKETSHIP for both preclinical and clinical studies is shown using DCE-MRI studies of the human brain and a murine tumor model. Conclusion: A DCE-MRI software suite was implemented and tested using simulations. Its applicability to both preclinical and clinical datasets is shown. ROCKETSHIP was designed to be easily accessible for the beginner, but flexible enough for changes or additions to be made by the advanced user as well. The availability of a flexible analysis tool will aid future studies using DCE-MRI

MITK-ModelFit: A generic open-source framework for model fits and their exploration in medical imaging -- design, implementation and application on the example of DCE-MRI

Many medical imaging techniques utilize fitting approaches for quantitative parameter estimation and analysis. Common examples are pharmacokinetic modeling in DCE MRI/CT, ADC calculations and IVIM modeling in diffusion-weighted MRI and Z-spectra analysis in chemical exchange saturation transfer MRI. Most available software tools are limited to a special purpose and do not allow for own developments and extensions. Furthermore, they are mostly designed as stand-alone solutions using external frameworks and thus cannot be easily incorporated natively in the analysis workflow. We present a framework for medical image fitting tasks that is included in MITK, following a rigorous open-source, well-integrated and operating system independent policy. Software engineering-wise, the local models, the fitting infrastructure and the results representation are abstracted and thus can be easily adapted to any model fitting task on image data, independent of image modality or model. Several ready-to-use libraries for model fitting and use-cases, including fit evaluation and visualization, were implemented. Their embedding into MITK allows for easy data loading, pre- and post-processing and thus a natural inclusion of model fitting into an overarching workflow. As an example, we present a comprehensive set of plug-ins for the analysis of DCE MRI data, which we validated on existing and novel digital phantoms, yielding competitive deviations between fit and ground truth. Providing a very flexible environment, our software mainly addresses developers of medical imaging software that includes model fitting algorithms and tools. Additionally, the framework is of high interest to users in the domain of perfusion MRI, as it offers feature-rich, freely available, validated tools to perform pharmacokinetic analysis on DCE MRI data, with both interactive and automatized batch processing workflows.Comment: 31 pages, 11 figures URL: http://mitk.org/wiki/MITK-ModelFi

Advanced signal processing methods in dynamic contrast enhanced magnetic resonance imaging

Tato dizertační práce představuje metodu zobrazování perfúze magnetickou rezonancí, jež je výkonným nástrojem v diagnostice, především v onkologii. Po ukončení sběru časové sekvence T1-váhovaných obrazů zaznamenávajících distribuci kontrastní látky v těle začíná fáze zpracování dat, která je předmětem této dizertace. Je zde představen teoretický základ fyziologických modelů a modelů akvizice pomocí magnetické rezonance a celý řetězec potřebný k vytvoření obrazů odhadu parametrů perfúze a mikrocirkulace v tkáni. Tato dizertační práce je souborem uveřejněných prací autora přispívajícím k rozvoji metodologie perfúzního zobrazování a zmíněného potřebného teoretického rozboru.This dissertation describes quantitative dynamic contrast enhanced magnetic resonance imaging (DCE-MRI), which is a powerful tool in diagnostics, mainly in oncology. After a time series of T1-weighted images recording contrast-agent distribution in the body has been acquired, data processing phase follows. It is presented step by step in this dissertation. The theoretical background in physiological and MRI-acquisition modeling is described together with the estimation process leading to parametric maps describing perfusion and microcirculation properties of the investigated tissue on a voxel-by-voxel basis. The dissertation is divided into this theoretical analysis and a set of publications representing particular contributions of the author to DCE-MRI.

Noninvasive monitoring of radiotherapy-induced microvascular changes using dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) in a colorectal tumor model

To examine dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) with a macromolecular contrast agent (P792) to visualize effects of radiotherapy (RT) on microvascular leakage in a colorectal cancer model.Journal Articleinfo:eu-repo/semantics/publishe

Model Agnostic Saliency for Weakly Supervised Lesion Detection from Breast DCE-MRI

There is a heated debate on how to interpret the decisions provided by deep learning models (DLM), where the main approaches rely on the visualization of salient regions to interpret the DLM classification process. However, these approaches generally fail to satisfy three conditions for the problem of lesion detection from medical images: 1) for images with lesions, all salient regions should represent lesions, 2) for images containing no lesions, no salient region should be produced,and 3) lesions are generally small with relatively smooth borders. We propose a new model-agnostic paradigm to interpret DLM classification decisions supported by a novel definition of saliency that incorporates the conditions above. Our model-agnostic 1-class saliency detector (MASD) is tested on weakly supervised breast lesion detection from DCE-MRI, achieving state-of-the-art detection accuracy when compared to current visualization methods

Functional imaging and circulating biomarkers of response to regorafenib in treatment-refractory metastatic colorectal cancer patients in a prospective phase II study

open32Regorafenib demonstrated efficacy in patients with metastatic colorectal cancer (mCRC). Lack of predictive biomarkers, potential toxicities and cost-effectiveness concerns highlight the unmet need for better patient selection.openKhan, Khurum; Rata, Mihaela; Cunningham, David; Koh, Dow-Mu; Tunariu, Nina; Hahne, Jens C; Vlachogiannis, George; Hedayat, Somaieh; Marchetti, Silvia; Lampis, Andrea; Damavandi, Mahnaz Darvish; Lote, Hazel; Rana, Isma; Williams, Anja; Eccles, Suzanne A; Fontana, Elisa; Collins, David; Eltahir, Zakaria; Rao, Sheela; Watkins, David; Starling, Naureen; Thomas, Jan; Kalaitzaki, Eleftheria; Fotiadis, Nicos; Begum, Ruwaida; Bali, Maria; Rugge, Massimo; Temple, Eleanor; Fassan, Matteo; Chau, Ian; Braconi, Chiara; Valeri, NicolaKhan, Khurum; Rata, Mihaela; Cunningham, David; Koh, Dow-Mu; Tunariu, Nina; Hahne, Jens C; Vlachogiannis, George; Hedayat, Somaieh; Marchetti, Silvia; Lampis, Andrea; Damavandi, Mahnaz Darvish; Lote, Hazel; Rana, Isma; Williams, Anja; Eccles, Suzanne A; Fontana, Elisa; Collins, David; Eltahir, Zakaria; Rao, Sheela; Watkins, David; Starling, Naureen; Thomas, Jan; Kalaitzaki, Eleftheria; Fotiadis, Nicos; Begum, Ruwaida; Bali, Maria; Rugge, Massimo; Temple, Eleanor; Fassan, Matteo; Chau, Ian; Braconi, Chiara; Valeri, Nicol

Automatic Renal Segmentation in DCE-MRI using Convolutional Neural Networks

Kidney function evaluation using dynamic contrast-enhanced MRI (DCE-MRI) images could help in diagnosis and treatment of kidney diseases of children. Automatic segmentation of renal parenchyma is an important step in this process. In this paper, we propose a time and memory efficient fully automated segmentation method which achieves high segmentation accuracy with running time in the order of seconds in both normal kidneys and kidneys with hydronephrosis. The proposed method is based on a cascaded application of two 3D convolutional neural networks that employs spatial and temporal information at the same time in order to learn the tasks of localization and segmentation of kidneys, respectively. Segmentation performance is evaluated on both normal and abnormal kidneys with varying levels of hydronephrosis. We achieved a mean dice coefficient of 91.4 and 83.6 for normal and abnormal kidneys of pediatric patients, respectively

DCE-MRI and parametric imaging in monitoring response to neoadjuvant chemotherapy in breast carcinoma : a preliminary report

Purpose: Neoadjuvant chemotherapy is recommended in patients with locally advanced breast cancer. Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) enables evaluation of the tumour neovasculature that occurs prior to any volume change, which helps identify early treatment failures and allows prompt implementation of second-line therapy. Material and methods: We conducted a prospective study in 14 patients with histopathologically proven breast cancer. DCE-MRI data were acquired using multisection, T1-weighted, 3D vibe sequences with fat suppression before, during, and after IV bolus injection (0.1 mmol/kg body weight, Gadoversetamide, Optimark). Post-processing of dynamic contrast perfusion data was done with the vendor's Tissue 4D software to generate various dynamic contrast parameters, i.e. Ktrans, Kep, Ve, initial area under the time signal curve (IAUC), apparent diffusion coefficient (ADC), and enhancement curve. Patients underwent MRI examinations at baseline, and then after two cycles, and finally at completion of chemotherapy. Results: Based on Sataloff criteria for pathological responses, four patients out of 14 were responders, and 10 were non-responders. At the 2nd MRI examination, IAUC was significantly smaller in responders than in non-responders (p = 0.023). When the results of the first and second MRI examinations were compared, Kep decreased from baseline to the second MRI (p = 0.03) in non-responders and in responders (p = 0.04). This change was statistically significant in both groups. The ADC values increased significantly in responders from baseline to the third MRI (p = 0.012). Conclusions: In our study, IAUC and ADC were the only parameters that reliably differentiated responders from non-responders after two and three cycles of chemotherapy