An open source software for analysis of dynamic contrast enhanced magnetic resonance images: UMMPerfusion revisited

Abstract

BackgroundPerfusion imaging has become an important image based tool to derive the physiological information in various applications, like tumor diagnostics and therapy, stroke, (cardio-) vascular diseases, or functional assessment of organs. However, even after 20 years of intense research in this field, perfusion imaging still remains a research tool without a broad clinical usage. One problem is the lack of standardization in technical aspects which have to be considered for successful quantitative evaluation; the second problem is a lack of tools that allow a direct integration into the diagnostic workflow in radiology.ResultsFive compartment models, namely, a one compartment model (1CP), a two compartment exchange (2CXM), a two compartment uptake model (2CUM), a two compartment filtration model (2FM) and eventually the extended Toft’s model (ETM) were implemented as plugin for the DICOM workstation OsiriX. Moreover, the plugin has a clean graphical user interface and provides means for quality management during the perfusion data analysis. Based on reference test data, the implementation was validated against a reference implementation. No differences were found in the calculated parameters.ConclusionWe developed open source software to analyse DCE-MRI perfusion data. The software is designed as plugin for the DICOM Workstation OsiriX. It features a clean GUI and provides a simple workflow for data analysis while it could also be seen as a toolbox providing an implementation of several recent compartment models to be applied in research tasks. Integration into the infrastructure of a radiology department is given via OsiriX. Results can be saved automatically and reports generated automatically during data analysis ensure certain quality control.

Variability and Reproducibility of 3rd-generation dual-source dynamic volume perfusion CT Parameters in Comparison to MR-perfusion Parameters in Rectal Cancer

“…3 ) depending on the specific tumour position within the rectum using the Osirix DICOM viewer (Pixmeo, Geneva, Switzerland). Perfusion parameters were calculated employing the fast deconvolution algorithm using an in-house developed established perfusion plugin tool (UMMPerfusion) 23 . Plasma flow (PF) [mL/100 mL/min], plasma volume (PV) [mL/100 mL] and mean transit time (MTT) [s] were estimated in tumour tissue and normal rectal wall.…”

Color-coded visualization of magnetic resonance imaging multiparametric maps

“…After the 15 th volume, 0.05 ml of contrast agent (Dotarem, Guerbet, France) was manually administered in the femoral vein, followed by a 1.0 ml saline flush. Of the acquired data the parametric maps of the Plasma flow, Plasma Volume and Tubular flow were calculated using an in house certified OsiriX plugin (UMMperfusion 1.5.2)1819.…”

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

“…Several open-source packages for analysis of DCE MRI data have been presented in the last years [24,25,26,27,28,29,30,31]. They can be divided into two categories: stand-alone tools, designed explicitly and only for DCE MRI analysis, and plug-ins or packages, that provide the analysis functionality within a larger analysis framework.…”

“…Thus, OsiriX plug-ins for DCE MRI analysis, e.g. UMMPerfusion [31] and the DCETool [29], are popular tools that can be used for an entire radiological workflow. However, OsiriX is only available on Mac OS, which presents another drawback.…”

“…The model-view-controller (MVC) pattern [43] and its variations are well-known strategies to decouple parts of an application and to allow thorough separation of concerns. It has been applied in other solutions [44]. In our implementations based on MITK, a MVC pattern with multiple views and controllers was applied.…”