Density Compensated Unrolled Networks for Non-Cartesian MRI Reconstruction

Deep neural networks have recently been thoroughly investigated as a powerful tool for MRI reconstruction. There is a lack of research, however, regarding their use for a specific setting of MRI, namely non-Cartesian acquisitions. In this work, we introduce a novel kind of deep neural networks to tackle this problem, namely density compensated unrolled neural networks, which rely on Density Compensation to correct the uneven weighting of the k-space. We assess their efficiency on the publicly available fastMRI dataset, and perform a small ablation study. Our results show that the density-compensated unrolled neural networks outperform the different baselines, and that all parts of the design are needed. We also open source our code, in particular a Non-Uniform Fast Fourier transform for TensorFlow.

Reference: Z. Ramzi,  J.-L. Starck and P. Ciuciu “Density Compensated Unrolled Networks for Non-Cartesian MRI Reconstruction.

This conference paper presents an adaptation of unrolled networks to the challenging setup of Non-Cartesian MRI Reconstruction. It also introduces the implementation of the Non-Uniform Fast Fourier Transform in TensorFlow: tfkbnufft.
It has been accepted at ISBI 2021.

State-of-the-art Machine Learning MRI Reconstruction in 2020: Results of the Second fastMRI Challenge

Accelerating MRI scans is one of the principal outstanding problems in the MRI research community. Towards this goal, we hosted the second fastMRI competition targeted towards reconstructing MR images with subsampled k-space data. We provided participants with data from 7,299 clinical brain scans (de-identified via a HIPAA-compliant procedure by NYU Langone Health), holding back the fully-sampled data from 894 of these scans for challenge evaluation purposes. In contrast to the 2019 challenge, we focused our radiologist evaluations on pathological assessment in brain images. We also debuted a new Transfer track that required participants to submit models evaluated on MRI scanners from outside the training set. We received 19 submissions from eight different groups. Results showed one team scoring best in both SSIM scores and qualitative radiologist evaluations. We also performed analysis on alternative metrics to mitigate the effects of background noise and collected feedback from the participants to inform future challenges. Lastly, we identify common failure modes across the submissions, highlighting areas of need for future research in the MRI reconstruction community.

Reference: Mathew J. Muckley, ...,   Z. Ramzi,  P. Ciuciu and J.-L. Starck et al . “State-of-the-art Machine Learning MRI Reconstruction in 2020: Results of the Second fastMRI Challenge.

This paper presents the results of the fastMRI 2020 challenge, where our team finished 2nd in the 4x and 8x supervised tracks.
It is currently being submitted to IEEE TMI.

XPDNet for MRI Reconstruction: an Application to the fastMRI 2020 Brain Challenge

We present a modular cross-domain neural network the XPDNet and its application to the MRI reconstruction task. This approach consists in unrolling the PDHG algorithm as well as learning the acceleration scheme between steps. We also adopt state-of-the-art techniques specific to Deep Learning for MRI reconstruction. At the time of writing, this approach is the best performer in PSNR on the fastMRI leaderboards for both knee and brain at acceleration factor 4.

Reference:  Z. Ramzi,  P. Ciuciu and J.-L. Starck . “XPDNet for MRI Reconstruction: an Application to the fastMRI 2020 Brain Challenge.

 

This network was used to submit reconstructions to the 2020 fastMRI Brain reconstruction challenge. Results are to be announced on December 6th 2020.

Denoising Score-Matching for Uncertainty Quantification in Inverse Problems

Deep neural networks have proven extremely efficient at solving a wide range of inverse problems, but most often the uncertainty on the solution they provide is hard to quantify. In this work, we propose a generic Bayesian framework for solving inverse problems, in which we limit the use of deep neural networks to learning a prior distribution on the signals to recover. We adopt recent denoising score matching techniques to learn this prior from data, and subsequently use it as part of an annealed Hamiltonian Monte-Carlo scheme to sample the full posterior of image inverse problems. We apply this framework to Magnetic Resonance Image (MRI) reconstruction and illustrate how this approach not only yields high quality reconstructions but can also be used to assess the uncertainty on particular features of a reconstructed image.

Reference:  Z. Ramzi,  Benjamin Remy, François Lanusse, J.-L. Starck and P. Ciuciu. “Denoising Score-Matching for Uncertainty Quantification in Inverse Problems, Deep Learning and Inverse Problems Workshop NeurIPS, 2020.

Wavelets in the Deep Learning Era

Sparsity based methods, such as wavelets, have been state-of-the-art for more than 20 years for inverse problems before being overtaken by neural networks.
In particular, U-nets have proven to be extremely effective.
Their main ingredients are a highly non-linear processing, a massive learning made possible by the flourishing of optimization algorithms with the power of computers (GPU) and the use of large available data sets for training.
While the many stages of non-linearity are intrinsic to deep learning, the usage of learning with training data could also be exploited by sparsity based approaches.
The aim of our study is to push the limits of sparsity with learning, and comparing the results with U-nets.
We present a new network architecture, which conserves the properties of sparsity based methods such as exact reconstruction and good generalization properties, while fostering the power of neural networks for learning and fast calculation.
We evaluate the model on image denoising tasks and show it is competitive with learning-based models.

Reference:  Z. Ramzi,  J.-L. Starck and P. Ciuciu. “Wavelets in the Deep Learning Era, Eusipco, 2020.

Benchmarking Deep Nets MRI Reconstruction Models on the FastMRI Publicly Available Dataset

 

The MRI reconstruction field lacked a proper data set that allowed for reproducible results on real raw data (i.e. complex-valued), especially when it comes to deep learning (DL) methods as this kind of approaches require much more data than classical Compressed Sensing~(CS) reconstruction. This lack is now filled by the fastMRI data set, and it is needed to evaluate recent DL models on this benchmark. Besides, these networks are written in different frameworks and repositories (if publicly available), it is therefore needed to have a common tool, publicly available, allowing a reproducible benchmark of the different methods and ease of building new models. We provide such a tool that allows the benchmark of different reconstruction deep learning models.

Reference:  Z. Ramzi, P. Ciuciu and J.-L. Starck. “Benchmarking Deep Nets MRI Reconstruction Models on the FastMRI Publicly Available Dataset, ISBI, 2020.

Recovery of 21-cm intensity maps with sparse component separation

 

Authors: I.P. Carucci, M.O. Irfan, J.Bobin
Journal: MNRAS
Year: 2020
Download: ADS | arXiv

21 cm intensity mapping has emerged as a promising technique to map the large-scale structure of the Universe. However, the presence of foregrounds with amplitudes orders of magnitude larger than the cosmological signal constitutes a critical challenge. In this work, we test the sparsity-based algorithm Generalised Morphological Component Analysis (GMCA) as a blind component separation technique for this class of experiments. We test the GMCA performance against realistic full-sky mock temperature maps that include, besides astrophysical foregrounds, also a fraction of the polarized part of the signal leaked into the unpolarized one, a very troublesome foreground to subtract, usually referred to as polarization leakage. To our knowledge, this is the first time the removal of such component is performed with no prior assumption. We assess the success of the cleaning by comparing the true and recovered power spectra, in the angular and radial directions. In the best scenario looked at, GMCA is able to recover the input angular (radial) power spectrum with an average bias of 5% for >25 (2030% for k_ll ≳ 0.02 Mpc/h), in the presence of polarization leakage. Our results are robust also when up to 40% of channels are missing, mimicking a Radio Frequency Interference (RFI) flagging of the data. Having quantified the notable effect of polarisation leakage on our results, in perspective we advocate the use of more realistic simulations when testing 21 cm intensity mapping capabilities.

Code and demonstrative notebooks are available here and data-set to reproduce our results is available here.

Semi-supervised dictionary learning with graph regularization and active points

 

Authors: Khanh-Hung TranFred-Maurice Ngole-Mboula, J-L. Starck
Journal: SIAM Journal on Imaging Sciences
Year: 2020
DOI: 10.1137/19M1285469
Download: arXiv


Abstract

Supervised Dictionary Learning has gained much interest in the recent decade and has shown significant performance improvements in image classification. However, in general, supervised learning needs a large number of labelled samples per class to achieve an acceptable result. In order to deal with databases which have just a few labelled samples per class, semi-supervised learning, which also exploits unlabelled samples in training phase is used. Indeed, unlabelled samples can help to regularize the learning model, yielding an improvement of classification accuracy. In this paper, we propose a new semi-supervised dictionary learning method based on two pillars: on one hand, we enforce manifold structure preservation from the original data into sparse code space using Locally Linear Embedding, which can be considered a regularization of sparse code; on the other hand, we train a semi-supervised classifier in sparse code space. We show that our approach provides an improvement over state-of-the-art semi-supervised dictionary learning methods
.