Fast Acquisition and Reconstruction Techniques in MRI

The aim of this thesis was to develop fast reconstruction and acquisition techniques for MRI that can support clinical applications where time is a limiting factor. In general, fast acquisition techniques were realized by undersampling k-space, while fast reconstruction techniques were achieved by using efficient numerical algorithms. In particular, undersampled acquisitions were processed in a CS and MRF framework. Preconditioning techniques were used to accelerate CS reconstructions, and a number of challenges encountered in MRF were addressed using appropriate post-processing techniques. European Research Council (ERC) Advanced Grant (670629 NOMA MRI)LUMC / Geneeskund

Image distortion correction for MRI in low field permanent magnet systems with strong B-0 inhomogeneity and gradient field nonlinearities

Objective To correct for image distortions produced by standard Fourier reconstruction techniques on low field permanent magnet MRI systems with strong B-0 inhomogeneity and gradient field nonlinearities. Materials and methods Conventional image distortion correction algorithms require accurate Delta B-0 maps which are not possible to acquire directly when the B-0 inhomogeneities also produce significant image distortions. Here we use a readout gradient time-shift in a TSE sequence to encode the B-0 field inhomogeneities in the k-space signals. Using a non-shifted and a shifted acquisition as input, Delta B-0 maps and images were reconstructed in an iterative manner. In each iteration, Delta B-0 maps were reconstructed from the phase difference using Tikhonov regularization, while images were reconstructed using either conjugate phase reconstruction (CPR) or model-based (MB) image reconstruction, taking the reconstructed field map into account. MB reconstructions were, furthermore, combined with compressed sensing (CS) to show the flexibility of this approach towards undersampling. These methods were compared to the standard fast Fourier transform (FFT) image reconstruction approach in simulations and measurements. Distortions due to gradient nonlinearities were corrected in CPR and MB using simulated gradient maps. Results Simulation results show that for moderate field inhomogeneities and gradient nonlinearities, Delta B-0 maps and images reconstructed using iterative CPR result in comparable quality to that for iterative MB reconstructions. However, for stronger inhomogeneities, iterative MB reconstruction outperforms iterative CPR in terms of signal intensity correction. Combining MB with CS, similar image and Delta B-0 map quality can be obtained without a scan time penalty. These findings were confirmed by experimental results. Discussion In case of B-0 inhomogeneities in the order of kHz, iterative MB reconstructions can help to improve both image quality and Delta B-0 map estimation.Radiolog

Stochastic neighbor embedding as a tool for visualizing the encoding capability of magnetic resonance fingerprinting dictionaries

Objective To visualize the encoding capability of magnetic resonance fingerprinting (MRF) dictionaries. Materials and methods High-dimensional MRF dictionaries were simulated and embedded into a lower-dimensional space using t-distributed stochastic neighbor embedding (t-SNE). The embeddings were visualized via colors as a surrogate for location in low-dimensional space. First, we illustrate this technique on three different MRF sequences. We then compare the resulting embeddings and the color-coded dictionary maps to these obtained with a singular value decomposition (SVD) dimensionality reduction technique. We validate the t-SNE approach with measures based on existing quantitative measures of encoding capability using the Euclidean distance. Finally, we use t-SNE to visualize MRF sequences resulting from an MRF sequence optimization algorithm. Results t-SNE was able to show clear differences between the color-coded dictionary maps of three MRF sequences. SVD showed smaller differences between different sequences. These findings were confirmed by quantitative measures of encoding. t-SNE was also able to visualize differences in encoding capability between subsequent iterations of an MRF sequence optimization algorithm. Discussion This visualization approach enables comparison of the encoding capability of different MRF sequences. This technique can be used as a confirmation tool in MRF sequence optimization.Radiolog

Regularized joint water-fat separation with B-0 map estimation in image space for 2D-navigated interleaved EPI based diffusion MRI

Purpose To develop a new water-fat separation and B-0 estimation algorithm to effectively suppress the multiple resonances of fat signal in EPI. This is especially relevant for DWI where fat is often a confounding factor. Methods Water-fat separation based on chemical-shift encoding enables robust fat suppression in routine MRI. However, for EPI the different chemical-shift displacements of the multiple fat resonances along the phase-encoding direction can be problematic for conventional separation algorithms. This work proposes a suitable model approximation for EPI under B-0 and fat off-resonance effects, providing a feasible multi-peak water-fat separation algorithm. Simulations were performed to validate the algorithm. In vivo validation was performed in 6 volunteers, acquiring spin-echo EPI images in the leg (B-0 homogeneous) and head-neck (B-0 inhomogeneous) regions, using a TE-shifted interleaved EPI sequence with/without diffusion sensitization. The results are numerically and statistically compared with voxel-independent water-fat separation and fat saturation techniques to demonstrate the performance of the proposed algorithm. Results The reference separation algorithm without the proposed spatial shift correction caused water-fat ambiguities in simulations and in vivo experiments. Some spectrally selective fat saturation approaches also failed to suppress fat in regions with severe B-0 inhomogeneities. The proposed algorithm was able to achieve improved fat suppression for DWI data and ADC maps in the head-neck and leg regions. Conclusion The proposed algorithm shows improved suppression of the multi-peak fat components in multi-shot interleaved EPI applications compared to the conventional fat saturation approaches and separation algorithms.Neuro Imaging ResearchRadiolog

In vivo 3D brain and extremity MRI at 50 mT using a permanent magnet Halbach array

Purpose To design a low-cost, portable permanent magnet-based MRI system capable of obtaining in vivo MR images within a reasonable scan time. Methods A discretized Halbach permanent magnet array with a clear bore diameter of 27 cm was designed for operation at 50 mT. Custom-built gradient coils, RF coil, gradient amplifiers, and RF amplifier were integrated and tested on both phantoms and in vivo. Results Phantom results showed that the gradient nonlinearity in the y-direction and z-direction was less than 5% over a 15-cm FOV and did not need correcting. For the x-direction, it was significantly greater, but could be partially corrected in postprocessing. Three-dimensional in vivo scans of the brain of a healthy volunteer using a turbo spin-echo sequence were acquired at a spatial resolution of 4 x 4 x 4 mm in a time of about 2 minutes. The T-1-weighted and T-2-weighted scans showed a good degree of tissue contrast. In addition, in vivo scans of the knee of a healthy volunteer were acquired at a spatial resolution of about 3 x 2 x 2 mm within 12 minutes to show the applicability of the system to extremity imaging. Conclusion This work has shown that it is possible to construct a low-field MRI unit with hardware components costing less than 10 000 Euros, which is able to acquire human images in vivo within a reasonable data-acquisition time. The system has a high degree of portability with magnet weight of approximately 75 kg, gradient and RF amplifiers each 15 kg, gradient coils 10 kg, and spectrometer 5 kg.Neuro Imaging Researc

Monitoring Fast Superconducting Qubit Dynamics Using A Neural Network

Weak measurements of a superconducting qubit produce noisy voltage signals that are weakly correlated with the qubit state. To recover individual quantum trajectories from these noisy signals, traditional methods require slow qubit dynamics and substantial prior information in the form of calibration experiments. Monitoring rapid qubit dynamics, e.g., during quantum gates, requires more complicated methods with increased demand for prior information. Here, we experimentally demonstrate an alternative method for accurately tracking rapidly driven superconducting qubit trajectories that uses a long short-term memory (LSTM) artificial neural network with minimal prior information. Despite few training assumptions, the LSTM produces trajectories that include qubit-readout resonator correlations due to a finite detection bandwidth. In addition to revealing rotated measurement eigenstates and a reduced measurement rate in agreement with theory for a fixed drive, the trained LSTM also correctly reconstructs evolution for an unknown drive with rapid modulation. Our work enables new applications of weak measurements with faster or initially unknown qubit dynamics, such as the diagnosis of coherent errors in quantum gates

A Hermetic On-Cryostat Helium Source for Low Temperature Experiments

We describe a helium source cell for use in cryogenic experiments that is hermetically sealed $in$ $situ$ on the cold plate of a cryostat. The source cell is filled with helium gas at room temperature and subsequently sealed using a cold weld crimping tool before the cryostat is closed and cooled down. At low temperature the helium condenses and collects in a connected experimental volume, as monitored via the frequency response of a planar superconducting resonator device sensitive to small amounts of liquid helium. This on-cryostat helium source negates the use of a filling tube between the cryogenic volumes and room temperature, thereby preventing unwanted effects such as such as temperature instabilities that arise from the thermomechanical motion of helium within the system. This helium source can be used in experiments investigating the properties of quantum fluids or to better thermalize quantum devices.Comment: 5 pages, 3 figure