ICM - Institut du Cerveau et de la Moelle épinière
Center for neuroimaging research (CENIR) – ICM
Paris/FR Itamar Ronen
C.J. Gorter Center for High Field MRI
Leiden University Medical Center
Molecular Imaging Research Center
Commissariat à l'énergie atomique et aux énergies alternatives (CEA)
Center for neuroimaging research (CENIR) – ICM
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F. Branzoli, I. Carson, R. Kreis, C. Ligneul, M. Palombo, I. Ronen, N. Shemesh, J. Valette
Goals of the Course
This course is designed to provide a strong practical foundation in the principles of diffusion weighted magnetic resonance spectroscopy (DW-MRS) in all of its aspects. DW-MRS provides unique cell-specific microstructural information based on the diffusion properties of intracellular metabolites in neural and muscle tissue, and it thus complements most sensitive but less specific methods such as diffusion tensor imaging (DTI). In clinical and preclinical research, incorporation of DW-MRS in a comprehensive protocol aimed at microstructural characterisation of tissue allows disentangling the effect of multiple pathological processes on tissue microstructure, and thus significantly increases the explanatory power of MR for the overall pathology.
At present, however, incorporation of DW-MRS in standard protocols poses significant challenges: robust DW-MRS sequences are not offered on any of the commercially available MR scanners. DW-MRS data acquisition is highly susceptible to physiological fluctuations, and the DW-MRS signal is strongly affected by e.g. eddy currents generated by the strong diffusion weighting gradients and cardiac pulsation. As a result, the robustness and reproducibility of DW-MRS strongly depends on a highly specialized pipeline of acquisition and processing that takes into account as many possible adverse effects as possible.
Attendees of the course are expected to have a good background in MR physics and be familiar with basic concepts in diffusion MR and in vivo MRS. A basic knowledge of MATLAB is preferred, and an acquaintance with principles of signal processing is advantageous.
The course will cover the entire process of generating robust and reproducible single-voxel and spectroscopic imaging DW-MRS data. We will present the pulse sequences used in DW-MRS, including the most recently introduced, and the optimal circumstances for using each of these, based on the goal of the study. We will then discuss the role of phase/amplitude navigators in DW-MRSI and strategies for real time re-acquisition of corrupted k-space DW-MRS data. Strategies and techniques for eddy current corrections will be discussed, including e.g. the use of singular value decomposition of the residual water signal. Ultimately, various modelling strategies of DW-MRS data will be presented, as well as how to incorporate information from other modalities such as DTI and tissue segmentation into the modelling of DWS data.
The course will consist of two parts: in the first, a series of lectures will cover the main methodological aspects in DW-MRS, from acquisition to analysis and modelling, and emerging neuroscience and clinical research applications. The second part is a fully hands-on section, where attendees will plan and execute a DW-MRS experiment, export the data and process it with a comprehensive MATLAB code for DW-MRS signal processing that will be provided to them, and finally will analyze the data to generate diffusion properties of the metabolites they measured in the experiment. DW-MRS experiments will be performed on a 3T PRISMA scanner. For the processing, attendees will be able to use the computers available at the center.
DW-MRS pulse sequences
• Optimised incorporation of diffusion weighting in standard SV-MRS sequences
• Minimisation of eddy currents and cross-terms with background gradients
• Isotropic DW-MRS
• 2D-DW-CSI: Challenges and the strategies for the use of navigators to minimize signal fluctuations
• Double diffusion encoding spectroscopy (DDES)
• Designing the right DW-MRS experiment to answer a specific question
Post-processing of DW-MRS data
• Major sources of error in DW-MRS data and their correction
• Strategies for optimal eddy current correction for SV and 2D-DW-CSI data
• The subtle art of cardiac triggering and other prospective motion correction strategies
• Spectral quantification
Modelling and analysis
• Obtaining standard diffusion metrics from DW-MRS data
• Incorporation of models of cellular geometry for obtaining further information about cellular microstructure
• Incorporation of data from other MR modalities (DTI) for refining and increasing the amount of microstructural information from DW-MRS
Emerging neuroscience and clinical research applications
• Attendees and faculty will present and discuss emerging DW-MRS applications in basic science and clinical research