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

BMC Bioinformatics

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[1] 0000 0004 0492 0584, grid.7497.d, Division of Medical Image Computing, German Cancer Research Center DKFZ, Heidelberg, Germany;0000 0004 0492 0584, grid.7497.d, German Cancer Consortium (DKTK), Heidelberg, Germany;0000 0004 0492 0584, grid.7497.d, Department of Translational Radiation Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany;0000 0001 0328 4908, grid.5253.1, Department of Radiation Oncology, Heidelberg Ion-Beam Therapy Center (HIT), Heidelberg University Hospital, Heidelberg, Germany;0000 0001 0328 4908, grid.5253.1, National Center for Tumor Diseases (NCT), Heidelberg, Germany;grid.488831.e, Heidelberg Institute of Radiation Oncology (HIRO), Heidelberg, Germany;Department of Radiology, University Hospital Munich, Ludwig-Maximilians-University Munich, Munich, Germany;grid.488831.e, Heidelberg Institute of Radiation Oncology (HIRO), Heidelberg, Germany;0000 0004 0492 0584, grid.7497.d, Division of Medical Image Computing, German Cancer Research Center DKFZ, Heidelberg, Germany;grid.488831.e, Heidelberg Institute of Radiation Oncology (HIRO), Heidelberg, Germany;0000 0004 0492 0584, grid.7497.d, Division of Medical Image Computing, German Cancer Research Center DKFZ, Heidelberg, Germany;0000 0001 0328 4908, grid.5253.1, Section Pattern Recognition, Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, Germany;

关键词: Pharmacokinetic modeling;    Tracer-kinetics;    Dynamic PET;    Multi-purpose;    Software development;    Model fitting;   

DOI  :  10.1186/s12859-018-2588-1

来源: publisher

【 摘 要 】

BackgroundMany medical imaging techniques utilize fitting approaches for quantitative parameter estimation and analysis. Common examples are pharmacokinetic modeling in dynamic contrast-enhanced (DCE) magnetic resonance imaging (MRI)/computed tomography (CT), apparent diffusion coefficient calculations and intravoxel incoherent motion 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.ResultsWe present a framework for medical image fitting tasks that is included in the Medical Imaging Interaction Toolkit 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.ConclusionsProviding 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.

【 授权许可】

CC BY