Data preparation protocol for low signal-to-noise ratio fluorine-19 MRI

Fluorine-19 MRI shows great promise for a wide range of applications including renal imaging, yet the typically low signal-to-noise ratios and sparse signal distribution necessitate a thorough data preparation.This chapter describes a general data preparation workflow for fluorine MRI experiments. The main processing steps are: (1) estimation of noise level, (2) correction of noise-induced bias and (3) background subtraction. The protocol is supplemented by an example script and toolbox available online.This chapter is based upon work from the COST Action PARENCHIMA, a community-driven network funded by the European Cooperation in Science and Technology (COST) program of the European Union, which aims to improve the reproducibility and standardization of renal MRI biomarkers. This analysis protocol chapter is complemented by two separate chapters describing the basic concept and experimental procedure

Sodium MRI of the human heart at 7.0 T: preliminary results

The objective of this work was to examine the feasibility of three-dimensional (3D) and whole heart coverage 23Na cardiac MRI at 7.0 T including single-cardiac-phase and cinematic (cine) regimes. A four-channel transceiver RF coil array tailored for 23Na MRI of the heart at 7.0 T (f = 78.5 MHz) is proposed. An integrated bow-tie antenna building block is used for 1H MR to support shimming, localization and planning in a clinical workflow. Signal absorption rate simulations and assessment of RF power deposition were performed to meet the RF safety requirements. 23Na cardiac MR was conducted in an in vivo feasibility study. 3D gradient echo (GRE) imaging in conjunction with Cartesian phase encoding (total acquisition time TAQ = 6 min 16 s) and whole heart coverage imaging employing a density-adapted 3D radial acquisition technique (TAQ = 18 min 20 s) were used. For 3D GRE-based 23Na MRI, acquisition of standard views of the heart using a nominal in-plane resolution of (5.0 x 5.0) mm2 and a slice thickness of 15 mm were feasible. For whole heart coverage 3D density-adapted radial 23Na acquisitions a nominal isotropic spatial resolution of 6 mm was accomplished. This improvement versus 3D conventional GRE acquisitions reduced partial volume effects along the slice direction and enabled retrospective image reconstruction of standard or arbitrary views of the heart. Sodium cine imaging capabilities were achieved with the proposed RF coil configuration in conjunction with 3D radial acquisitions and cardiac gating. Cardiac-gated reconstruction provided an enhancement in blood-myocardium contrast of 20% versus the same data reconstructed without cardiac gating. The proposed transceiver array enables 23Na MR of the human heart at 7.0 T within clinical acceptable scan times. This capability is in positive alignment with the needs of explorations that are designed to examine the potential of 23Na MRI for the assessment of cardiovascular and metabolic diseases

Denoising for improved parametric MRI of the kidney: protocol for nonlocal means filtering

In order to tackle the challenges caused by the variability in estimated MRI parameters (e.g., T(2)* and T(2)) due to low SNR a number of strategies can be followed. One approach is postprocessing of the acquired data with a filter. The basic idea is that MR images possess a local spatial structure that is characterized by equal, or at least similar, noise-free signal values in vicinities of a location. Then, local averaging of the signal reduces the noise component of the signal. In contrast, nonlocal means filtering defines the weights for averaging not only within the local vicinity, bur it compares the image intensities between all voxels to define "nonlocal" weights. Furthermore, it generally compares not only single-voxel intensities but small spatial patches of the data to better account for extended similar patterns. Here we describe how to use an open source NLM filter tool to denoise 2D MR image series of the kidney used for parametric mapping of the relaxation times T(2)* and T(2).This chapter is based upon work from the COST Action PARENCHIMA, a community-driven network funded by the European Cooperation in Science and Technology (COST) program of the European Union, which aims to improve the reproducibility and standardization of renal MRI biomarkers