Non-Cartesian 3D-SPARKLING vs Cartesian 3D-EPI encoding schemes for functional Magnetic Resonance Imaging at 7 Tesla.

The quest for higher spatial and/or temporal resolution in functional MRI (fMRI) while preserving a sufficient temporal signal-to-noise ratio (tSNR) has generated a tremendous amount of methodological contributions in the last decade ranging from Cartesian vs. non-Cartesian readouts, 2D vs. 3D acquisition strategies, parallel imaging and/or compressed sensing (CS) accelerations and simultaneous multi-slice acquisitions to cite a few. In this paper, we investigate the use of a finely tuned version of 3D-SPARKLING. This is a non-Cartesian CS-based acquisition technique for high spatial resolution whole-brain fMRI. We compare it to state-of-the-art Cartesian 3D-EPI during both a retinotopic mapping paradigm and resting-state acquisitions at 1mm3 (isotropic spatial resolution). This study involves six healthy volunteers and both acquisition sequences were run on each individual in a randomly-balanced order across subjects. The performances of both acquisition techniques are compared to each other in regards to tSNR, sensitivity to the BOLD effect and spatial specificity. Our findings reveal that 3D-SPARKLING has a higher tSNR than 3D-EPI, an improved sensitivity to detect the BOLD contrast in the gray matter, and an improved spatial specificity. Compared to 3D-EPI, 3D-SPARKLING yields, on average, 7% more activated voxels in the gray matter relative to the total number of activated voxels.

Impact of B 0 $$ {\mathrm{B}}_0 $$ field imperfections correction on BOLD sensitivity in 3D-SPARKLING fMRI data.

PURPOSE: Static and dynamic B 0 $$ {\mathrm{B}}_0 $$ field imperfections are detrimental to functional MRI (fMRI) applications, especially at ultra-high magnetic fields (UHF). In this work, a field camera is used to assess the benefits of retrospectively correcting B 0 $$ {\mathrm{B}}_0 $$ field perturbations on Blood Oxygen Level Dependent (BOLD) sensitivity in non-Cartesian three-dimensional (3D)-SPARKLING fMRI acquisitions. METHODS: fMRI data were acquired at 1 mm 3 $$ {}^3 $$ and for a 2.4s-TR while concurrently monitoring in real-time field perturbations using a Skope Clip-on field camera in a novel experimental setting involving a shorter TR than the required minimal TR of the field probes. Measurements of the dynamic field deviations were used along with a static Δ B 0 $$ \Delta {\mathrm{B}}_0 $$ map to retrospectively correct static and dynamic field imperfections, respectively. In order to evaluate the impact of such a correction on fMRI volumes, a comparative study was conducted on healthy volunteers. RESULTS: Correction of B 0 $$ {\mathrm{B}}_0 $$ deviations improved image quality and yielded between 20% and 30% increase in median temporal signal-to-noise ratio (tSNR).Using fMRI data collected during a retinotopic mapping experiment, we demonstrated a significant increase in sensitivity to the BOLD contrast and improved accuracy of the BOLD phase maps: 44% (resp., 159%) more activated voxels were retrieved when using a significance control level based on a p-value of 0.001 without correcting for multiple comparisons (resp., 0.05 with a false discovery rate correction). CONCLUSION: 3D-SPARKLING fMRI hugely benefits from static and dynamic B 0 $$ {\mathrm{B}}_0 $$ imperfections correction. However, the proposed experimental protocol is flexible enough to be deployed on a large spectrum of encoding schemes, including arbitrary non-Cartesian readouts.

Deep learning-assisted model-based off-resonance correction for non-Cartesian SWI.

PURPOSE: Patient-induced inhomogeneities in the static magnetic field cause distortions and blurring (off-resonance artifacts) during acquisitions with long readouts such as in SWI. Conventional versatile correction methods based on extended Fourier models are too slow for clinical practice in computationally demanding cases such as 3D high-resolution non-Cartesian multi-coil acquisitions. THEORY: Most reconstruction methods can be accelerated when performing off-resonance correction by reducing the number of iterations, compressed coils, and correction components. Recent state-of-the-art unrolled deep learning architectures could help but are generally not adapted to corrupted measurements as they rely on the standard Fourier operator in the data consistency term. The combination of correction models and neural networks is therefore necessary to reduce reconstruction times. METHODS: Hybrid pipelines using UNets were trained stack-by-stack over 99 SWI 3D SPARKLING 20-fold accelerated acquisitions at 0.6 mm isotropic resolution using different off-resonance correction methods. Target images were obtained using slow model-based corrections based on self-estimated Δ B 0 $$ \Delta {B}_0 $$ field maps. The proposed strategies, tested over 11 volumes, are compared to model-only and network-only pipelines. RESULTS: The proposed hybrid pipelines achieved scores competing with two to three times slower baseline methods, and neural networks were observed to contribute both as pre-conditioner and through inter-iteration memory by allowing more degrees of freedom over the model design. CONCLUSION: A combination of model-based and network-based off-resonance correction was proposed to significantly accelerate conventional methods. Different promising synergies were observed between acceleration factors (iterations, coils, correction) and model/network that could be expanded in the future.

Improving spreading projection algorithm for rapid k-space sampling trajectories through minimized off-resonance effects and gridding of low frequencies.

PURPOSE: Non-Cartesian MRI with long arbitrary readout directions are susceptible to off-resonance artifacts due to patient induced B 0 $$ {B}_0 $$ inhomogeneities. This results in degraded image quality with strong signal losses and blurring. Current solutions to address this issue involve correcting the off-resonance artifacts during image reconstruction or reducing inhomogeneities through improved shimming. THEORY: The recently developed SPARKLING algorithm is extended to drastically diminish off-resonance artifacts by generating temporally smooth k-space sampling patterns. For doing so, the cost function which is optimized in SPARKLING is modified using a temporal weighting factor. Additionally, oversampling of the center of k-space beyond the Nyquist criteria is prevented through the use of gridded sampling in the region, enforced with affine constraints. METHODS: Prospective k-space data was acquired at 3 T on new trajectories, and we show robustness to B 0 $$ {\mathrm{B}}_0 $$ inhomogeneities through in silico experiments by adding Δ B 0 $$ \Delta {\mathrm{B}}_0 $$  through artificial degradation of system B 0 $$ {\mathrm{B}}_0 $$ shimming. Later on, in vivo experiments were carried out to optimize parameters of the new improvements and benchmark the gain in performance. RESULTS: The improved trajectories allowed for the recovery of signal dropouts observed on original SPARKLING acquisitions at larger B 0 $$ {\mathrm{B}}_0 $$ field inhomogeneities. Furthermore, imposing gridded sampling at the center of k-space provided improved reconstructed image quality with limited artifacts. CONCLUSION: These advancements allowed us for nearly 4 . 62 × $$ 4.62\times $$ shorter scan time compared to GRAPPA-p4x1, allowing us to reach 600 µm isotropic resolution in 3D T 2 ∗ $$ {\mathrm{T}}_2^{\ast } $$ -w imaging in just 3.3 min at 3 T with negligible degradation in image quality.

Iterative static field map estimation for off-resonance correction in non-Cartesian susceptibility weighted imaging.

PURPOSE: Patient-induced inhomogeneities in the magnetic field cause distortions and blurring during acquisitions with long readouts such as in susceptibility-weighted imaging (SWI). Most correction methods require collecting an additional ΔB0$$ \Delta {\mathrm{B}}_0 $$ field map to remove these artifacts. THEORY: The static ΔB0$$ \Delta {\mathrm{B}}_0 $$ field map can be approximated with an acceptable error directly from a single echo acquisition in SWI. The main component of the observed phase is linearly related to ΔB0$$ \Delta {\mathrm{B}}_0 $$ and the echo time (TE), and the relative impact of non- ΔB0$$ \Delta {\mathrm{B}}_0 $$ terms becomes insignificant with TE$$ \mathrm{TE} $$ >20 ms at 3 T for a well-tuned system. METHODS: The main step is to combine and unfold the multi-channel phase maps wrapped many times, and several competing algorithms are compared for this purpose. Four in vivo brain data sets collected using the recently proposed 3D spreading projection algorithm for rapid k-space sampling (SPARKLING) readouts are used to assess the proposed method. RESULTS: The estimated 3D field maps generated with a 0.6 mm isotropic spatial resolution provide overall similar off-resonance corrections compared to reference corrections based on an external ΔB0$$ \Delta {\mathrm{B}}_0 $$ acquisitions, and even improved for 2 of 4 individuals. Although a small estimation error is expected, no aftermath was observed in the proposed corrections, whereas degradations were observed in the references. CONCLUSION: A static ΔB0$$ \Delta {\mathrm{B}}_0 $$ field map estimation method was proposed to take advantage of acquisitions with long echo times, and outperformed the reference technique based on an external field map. The difference can be attributed to an inherent robustness to mismatches between volumes and external ΔB0$$ \Delta {\mathrm{B}}_0 $$ maps, and diverse other sources investigated.

Optimizing Full 3D SPARKLING Trajectories for High-Resolution Magnetic Resonance Imaging.

The Spreading Projection Algorithm for Rapid K-space sampLING, or SPARKLING, is an optimization-driven method that has been recently introduced for accelerated 2D MRI using compressed sensing. It has then been extended to address 3D imaging using either stacks of 2D sampling patterns or a local 3D strategy that optimizes a single sampling trajectory at a time. 2D SPARKLING actually performs variable density sampling (VDS) along a prescribed target density while maximizing sampling efficiency and meeting the gradient-based hardware constraints. However, 3D SPARKLING has remained limited in terms of acceleration factors along the third dimension if one wants to preserve a peaky point spread function (PSF) and thus good image quality. In this paper, in order to achieve higher acceleration factors in 3D imaging while preserving image quality, we propose a new efficient algorithm that performs optimization on full 3D SPARKLING. The proposed implementation based on fast multipole methods (FMM) allows us to design sampling patterns with up to 107 k-space samples, thus opening the door to 3D VDS. We compare multi-CPU and GPU implementations and demonstrate that the latter is optimal for 3D imaging in the high-resolution acquisition regime ( 600µ m isotropic). Finally, we show that this novel optimization for full 3D SPARKLING outperforms stacking strategies or 3D twisted projection imaging through retrospective and prospective studies on NIST phantom and in vivo brain scans at 3 Tesla taking the particular case of T2 *-w imaging. Overall the proposed method allows for 2.5-3.75x shorter scan times compared to GRAPPA-4 parallel imaging acquisition at 3 Tesla without compromising image quality.