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Compressed sensing in magnetic resonance imaging essentially involves the optimization of (1) the sampling pattern in k-space under MR hardware constraints and (2) image reconstruction from undersampled k-space data. Recently, deep learning methods have allowed the community to address both problems simultaneously, especially in the non-Cartesian acquisition setting. This work aims to contribute to this field by tackling some major concerns in existing approaches. Particularly, current state-of-the-art learning methods seek hardware compliant k-space sampling trajectories by enforcing the hardware constraints through additional penalty terms in the training loss. Through ablation studies, we rather show the benefit of using a projection step to enforce these constraints and demonstrate that the resulting k-space trajectories are more flexible under a projection-based scheme, which results in superior performance in reconstructed image quality. In 2D studies, our novel method trajectories present an improved image reconstruction quality at a 20-fold acceleration factor on the fastMRI data set with SSIM scores of nearly 0.92–0.95 in our retrospective studies as compared to the corresponding Cartesian reference and also see a 3–4 dB gain in PSNR as compared to earlier state-of-the-art methods. Finally, we extend the algorithm to 3D and by comparing optimization as learning-based projection schemes, we show that data-driven joint learning-based method trajectories outperform model-based methods such as SPARKLING through a 2 dB gain in PSNR and 0.02 gain in SSIM.

Whole brain estimation of the haemodynamic response function (HRF) in functional magnetic resonance imaging (fMRI) is critical to get insight on the global status of the neurovascular coupling of an individual in healthy or pathological condition. Most of existing approaches in the literature works on task-fMRI data and relies on the experimental paradigm as a surrogate of neural activity, hence remaining inoperative on resting-stage fMRI (rs-fMRI) data. To cope with this issue, recent works have performed either a two-step analysis to detect large neural events and then characterize the HRF shape or a joint estimation of both the neural and haemodynamic components in an univariate fashion. In this work, we express the neural activity signals as a combination of piece-wise constant temporal atoms associated with sparse spatial maps and introduce an haemodynamic parcellation of the brain featuring a temporally dilated version of a given HRF model in each parcel with unknown dilation parameters. We formulate the joint estimation of the HRF shapes and spatio-temporal neural representations as a multivariate semi-blind deconvolution problem in a paradigm-free setting and introduce constraints inspired from the dictionary learning literature to ease its identifiability. A fast alternating minimization algorithm, along with its efficient implementation, is proposed and validated on both synthetic and real rs-fMRI data at the subject level. To demonstrate its significance at the population level, we apply this new framework to the UK Biobank data set, first for the discrimination of haemodynamic territories between balanced groups (n=24 individuals in each) patients with an history of stroke and healthy controls and second, for the analysis of normal aging on the neurovascular coupling. Overall, we statistically demonstrate that a pathology like stroke or a condition like normal brain aging induce longer haemodynamic delays in certain brain areas (e.g. Willis polygon, occipital, temporal and frontal cortices) and that this haemodynamic feature may be predictive with an accuracy of 74 % of the individual’s age in a supervised classification task performed on n=459 subjects.

The analysis of human brain functional networks is achieved by computing functional connectivity indices reflecting phase coupling and interactions between remote brain regions. In magneto- and electroencephalography, the most frequently used functional connectivity indices are constructed based on Fourier-based cross-spectral estimation applied to specific fast and band-limited oscillatory regimes. Recently, infraslow arrhythmic fluctuations (below the 1 Hz) were recognized as playing a leading role in spontaneous brain activity. The present work aims to propose to assess functional connectivity from fractal dynamics, thus extending the assessment of functional connectivity to the infraslow arrhythmic or scale-free temporal dynamics of M/EEG-quantified brain activity. Instead of being based on Fourier analysis, new Imaginary Coherence and weighted Phase Lag indices are constructed from complex-wavelet representations. Their performances are first assessed on synthetic data by means of Monte-Carlo simulations, and they are then compared favorably against the classical Fourier-based indices. These new assessments of functional connectivity indices are also applied to MEG data collected on 36 individuals both at rest and during the learning of a visual motion discrimination task. They demonstrate a higher statistical sensitivity, compared to their Fourier counterparts, in capturing significant and relevant functional interactions in the infraslow regime and modulations from rest to task. Notably, the consistent overall increase in functional connectivity assessed from fractal dynamics from rest to task correlated with a change in temporal dynamics as well as with improved performance in task completion, which suggests that the complex-wavelet weighted Phase Lag index is the sole index is able to capture brain plasticity in the infraslow scale-free regime.

Our perceptual reality relies on inferences about the causal structure of the world given by multiple sensory inputs. In ecological settings, multisensory events that cohere in time and space benefit inferential processes: hearing and seeing a speaker enhances speech comprehension, and the acoustic changes of flapping wings naturally pace the motion of a flock of birds. Here, we asked how a few minutes of (multi)sensory training could shape cortical interactions in a subsequent unisensory perceptual task. For this, we investigated oscillatory activity and functional connectivity as a function of individuals’ sensory history during training. Human participants performed a visual motion coherence discrimination task while being recorded with magnetoencephalography. Three groups of participants performed the same task with visual stimuli only, while listening to acoustic textures temporally comodulated with the strength of visual motion coherence, or with auditory noise uncorrelated with visual motion. The functional connectivity patterns before and after training were contrasted to resting-state networks to assess the variability of common task-relevant networks, and the emergence of new functional interactions as a function of sensory history. One major finding is the emergence of a large-scale synchronization in the high γ (gamma: 60−120Hz) and β (beta: 15−30Hz) bands for individuals who underwent comodulated multisensory training. The post-training network involved prefrontal, parietal, and visual cortices. Our results suggest that the integration of evidence and decision-making strategies become more efficient following congruent multisensory training through plasticity in network routing and oscillatory regimes.

Over the last decade, the combination of compressed sensing (CS) with acquisition over multiple receiver coils in magnetic resonance imaging (MRI) has allowed the emergence of faster scans while maintaining a good signal-to-noise ratio (SNR). Self-calibrating techniques, such as ESPiRIT, have become the standard approach to estimating the coil sensitivity maps prior to the reconstruction stage. In this work, we proceed differently and introduce a new calibration-less multi-coil CS reconstruction method. Calibration-less techniques no longer require the prior extraction of sensitivity maps to perform multi-coil image reconstruction but usually alternate estimation sensitivity map estimation and image reconstruction. Here, to get rid of the nonconvexity of the latter approach we reconstruct as many MR images as the number of coils. To compensate for the ill-posedness of this inverse problem, we leverage structured sparsity of the multi-coil images in a wavelet transform domain while adapting to variations in SNR across coils owing to the OSCAR (octagonal shrinkage and clustering algorithm for regression) regularization. Coil-specific complex-valued MR images are thus obtained by minimizing a convex but nonsmooth objective function using the proximal primal-dual Condat-Vù algorithm. Comparison and validation on retrospective Cartesian and non-Cartesian studies based on the Brain fastMRI data set demonstrate that the proposed reconstruction method outperforms the state-of-the-art (ℓ1-ESPIRiT, calibration-less AC-LORAKS and CaLM methods) significantly on magnitude images for the T1 and FLAIR contrasts. Additionally, further validation operated on 8 to 20-fold prospectively accelerated high-resolution ex vivo human brain MRI data collected at 7 Tesla confirms the retrospective results. Overall, OSCAR-based regularization preserves phase information more accurately (both visually and quantitatively) compared to other approaches, an asset that can only be assessed on real prospective experiments.

Deep learning is starting to offer promising results for reconstruction in Magnetic Resonance Imaging (MRI). A lot of networks are being developed, but the comparisons remain hard because the frameworks used are not the same among studies, the networks are not properly re-trained, and the datasets used are not the same among comparisons. The recent release of a public dataset, fastMRI, consisting of raw k-space data, encouraged us to write a consistent benchmark of several deep neural networks for MR image reconstruction. This paper shows the results obtained for this benchmark, allowing to compare the networks, and links the open source implementation of all these networks in Keras. The main finding of this benchmark is that it is beneficial to perform more iterations between the image and the measurement spaces compared to having a deeper per-space network.