Estimating errors in clinical MRS

In clinical Magnetic Resonance Spectroscopy (MRS), errors in the estimated in vivo metabolite concentration are usually obtained from the Cramer-Rao lower bounds (CRBs). The reliability of this procedure under in vivo MRS conditions is discussed.ImPhysApplied Science

Magnetic resonance with La2 (Mg, Mn)3 (NO3) 12 . 24H2O

Applied Science

Java/JNI/C/Fortran makefile project for a Java plug-in and related Android app in Eclipse ADT bundle: A side-by-side comparison

We have developed a Java/Fortran based application, called MonteCarlo, that enables the users can carry out Monte Carlo studies in the field of in vivo MRS. The application is supposed to be used as a tool for the jMRUI platform, being the in vivo MRS software system of the TRANSACT European Union project. The MonteCarlo application can be launched either as a jMRUI custom plug-in (onWindows/Linux computers) or as a standalone Android app (on mobile Android devices). Both the plug-in and Android app version were developed as a Java/JNI/C/Fortran makefile project. This could be done by using one and the same version of Eclipse (in Eclipse ADT bundle), the main difference between the plug-in and Android app being the code, required for creating the GUI.ImPhys/Imaging PhysicsApplied Science

Monte Carlo Modeling for in vivo MRS: Generating and quantifying simulations via the Windows, Linux and Android platform

Work in context of European Union TRANSACT project. We have developed a Java/JNI/C/Fortran based software application, called MonteCarlo, with which the users can carry out Monte Carlo studies in the field of \emph{in vivo} MRS. The application is supposed to be used as a tool for supporting the \emph{j}MRUI platform, being the \emph{in vivo} MRS software system of the TRANSACT European Union project. The MonteCarlo application can be launched either as a \emph{j}MRUI custom plug-in (on Windows/Linux computers) or as a standalone Android app (on mobile devices with the Android platform). Both the MonteCarlo plug-in and the Android app version were developed as a Java/JNI/C/Fortran Makefile project by using one and the same version of the Eclipse Java IDE, the main difference between the two MonteCarlo versions being the codes, required for creating the GUI. We have tested the two versions of the MonteCarlo application with a few Monte Carlo studies, which enabled us to verify specific topics of \emph{in vivo} MRS Monte Carlo modeling, such as "parametric vs semi-parametric'' estimation, checking "Maximum Likelihood'' properties and dealing with the "Bias-Variance trade-off'' problem.ImPhysApplied Science

Java/JNI/C/Fortran based HSVD/HLSVD custom plugins for the jMRUI software system: Development, installation and usage

This work was done in the context of FP7 - PEOPLE Marie Curie Initial Training Network Project PITN-GA-2012-316679-TRANSACT. This report describes the development, installation and usage of the HSVD and HLSVD plugin for the jMRUI software system. The latter system is maintained by the TRANSACT EU project. The plugins aim at providing information for choosing the setup for the HSVD and HLSVD in vivo MRS quantification algorithm.Applied PhysicsApplied Science

Simulating Metabolite Basis Sets for in vivo MRS Quantification; Incorporating details of the PRESS Pulse Sequence by means of the GAMMA C++ library

In this work we report on generating/using simulated metabolite basis sets for the quantification of in vivo MRS signals, assuming that they have been acquired by using the PRESS pulse sequence. To that end we have employed the classes and functions of the GAMMA C++ library. By using several versions of our PRESS-simulation program, we were able to study the single-voxel selection, required for detecting in vivo MRS signals. Furthermore, by introducing in one of the versions a modified spatial summation scheme, that comes down to crusher-gradient averaging, we could realize a decrease in computation time by about a factor of 256. We have used four different simulated metabolite basis sets in the quantification of a real-world 3T human-brain 1H MRS signal. The best quantification is obtained, when including into the simulation program -as closely as possible- the related details of the PRESS-based single-voxel selectionImPhys/Imaging PhysicsApplied Science

Error-Bars in Semi-Parametric Estimation

In in vivo metabolite-quantitation with a magnetic resonance spectroscopy (MRS) scanner, the model function of the attendant MRS signal is often only partly known. This unfavourable condition requires semi-parametric estimation. In the present study the unknown part is the form of the decay function of the MRS signal. The lack of knowledge is caused by micro-heterogeneity of the tissue hosting the metabolites. At high magnetic field, i.e., 10 Tesla, it seems reasonable to assume that the decay function, although unknown, is the same for each metabolite species. As reported in Proc. ProRISC 2012, this assumption enabled us to circumvent the often cumbersome search in function space, normally required in semi-parametric estimation. Our present paper focuses on interpreting the semiparametric error bar provided by some leading metabolite quantitation packages. This is done by means of Monte Carlo simulations.ImPhys/Imaging PhysicsApplied Science

Dynamic MR-Imaging with Radial Scanning, a Post-Acquisition Keyhole Approach

A new method for 2D/3D dynamic MR-Imaging with radial scanning is proposed. It exploits the inherent strong oversampling in the centre of k-space, which holds crucial temporal information of the contrast evolution. It is based on (1) a rearrangement of (novel 3D) isotropic distributions of trajectories during the scan according to the desired time resolution and (2) a post-acquisition keyhole approach. The 2D/3D dynamic images are reconstructed using 2D/3D-gridding and 2D/3D-IFFT. The scan time is not increased with respect to a conventional 2D/3D radial scan of the same image resolution, in addition one benefits from the dynamic information. An application to in vivo ventilation of rat lungs using hyperpolarized helium is demonstrated.Applied Science

Improved estimation of the temporal decay function of in vivo metabolite signals

MRI-scanners enable non-invasive, in vivo quantitation of metabolites in, e.g., the brain of a patient. Among other things, this requires adequate estimation of the unknown temporal decay function of the complex-valued signal emanating from the metabolites. We propose a method to render a current decay estimator more simple, accurate, and robust, and test it on a simulated signal comprising contributions from ten metabolite species and scanner noise.ImPhys/Imaging PhysicsApplied Science