Biology subjects

Grussu, F.

Publications and source records attributed to Grussu, F..

3 recordsLinked to original sources

bioRxiv2020

Deep learning model fitting for diffusion-relaxometry: a comparative study

Quantitative Magnetic Resonance Imaging (qMRI) signal model fitting is traditionally performed via non-linear least square (NLLS) estimation. NLLS is slow and its performance can be affected by the presence of different local minima in the fitting objective function. Recently, machine learning techniques, including deep neural networks (DNNs), have been proposed as robust alternatives to NLLS. Here we present a deep learning implementation of qMRI model fitting, which uses DNNs to perform the inversion of the forward signal model. We compare two DNN training strategies, based on two alternative definitions of the loss function, since at present it is not known which definition leads to the most accurate, precise and robust parameter estimation. In strategy 1 we define the loss as the l2-norm of tissue parameter prediction errors, while in strategy 2 as the l2-norm of MRI signal prediction errors. We compare the two approaches on synthetic and 3T in vivo saturation inversion recovery (SIR) diffusion-weighted (DW) MRI data, using a model for joint diffusion-T1 mapping. Strategy 1 leads to lower tissue parameter root mean squared errors (RMSEs) when realistic noise distributions are considered (e.g. Rician vs Gaussian). However, strategy 2 offers lower signal reconstruction RMSE, and allows training to be performed on both synthetic and actual in vivo MRI measurements. In conclusion, both strategies are valid choices for DNN-based fitting. Strategy 2 is more practical, as it does not require pre-computation of reference tissue parameters, but may lead to worse parameter estimation.

neuroscience↗

bioRxiv2020

"Select and retrieve via direct upsampling" network (SARDU-Net): a data-driven, model-free, deep learning approach for quantitative MRI protocol design

PurposeWe introduce "Select and retrieve via direct upsampling" network (SARDU-Net), a data-driven framework for model-free quantitative MRI (qMRI) protocol design, and demonstrate it on in vivo brain and prostate diffusion-relaxation imaging (DRI). MethodsSARDU-Net selects subsets of informative measurements within lengthy pilot scans, without the requirement to identify tissue parameters for which to optimise for. The algorithm consists of a selector, identifying measurement subsets, and a predictor, estimating fully-sampled signals from the subsets. We implement both using deep neural networks, which are trained jointly end-to-end. We demonstrate the algorithm on brain (32 diffusion-/T1-weightings) and prostate (16 diffusion-/T2-weightings) DRI scans acquired on 3 healthy volunteers on two separate 3T Philips systems each. We used SARDU-Net to identify sub-protocols of fixed size, assessing the reproducibility of the procedure and testing sub-protocols for their potential to inform multi-contrast analyses via T1-weighted spherical mean diffusion tensor (T1-SMDT, brain) and hybrid multi-dimensional MRI (HM-MRI, prostate) modelling. ResultsIn both brain and prostate, SARDU-Net identifies sub-protocols that maximise information content in a reproducible manner across training instantiations. The sub-protocols enable multi-contrast modelling for which they were not optimised explicitly, providing robust T1-SMDT and HM-MRI maps and goodness-of-fit in the top 5% against extensive sub-protocol comparisons. ConclusionsSARDU-Net gives new opportunities to identify economical but informative qMRI protocols from a subset of the pilot scans that can be used for acquisition-time-sensitive applications. The simple architecture makes the algorithm easy to train when exhaustive searches are intractable, and applicable to a variety of anatomical contexts.

bioengineering↗

bioRxiv2019

Multi-parametric quantitative spinal cord MRI with unified signal readout and image denoising

Multi-parametric quantitative MRI (qMRI) of the spinal cord is a promising non-invasive tool to probe early microstructural damage in neurological disorders. It is usually performed by combining acquisitions with multiple signal readouts, which exhibit different thermal noise levels, geometrical distortions and susceptibility to physiological noise. This ultimately hinders joint multi-contrast modelling and makes the geometric correspondence of parametric maps challenging. We propose an approach to overcome these limitations, by implementing state-of-the-art microstructural MRI of the spinal cord with a unified signal readout. We base our acquisition on single-shot echo planar imaging with reduced field-of-view, and obtain data from two different vendors (vendor 1: Philips Achieva; vendor 2: Siemens Prisma). Importantly, the unified acquisition allows us to compare signal and noise across contrasts, thus enabling overall quality enhancement via Marchenko-Pastur (MP) Principal Component Analysis (PCA) denoising. MP-PCA is a recent method relying on redundant acquisitions, i.e. such that the number of measurements is much larger than the number of informative principal components. Here we used in vivo and synthetic data to test whether a unified readout enables more efficient denoising of less redundant acquisitions, since these can be denoised jointly with more redundant ones. We demonstrate that a unified readout provides robust multi-parametric maps, including diffusion and kurtosis tensors from diffusion MRI, myelin metrics from two-pool magnetisation transfer, and T1 and T2 from relaxometry. Moreover, we show that MP-PCA improves the quality of our multi-contrast acquisitions, since it reduces the coefficient of variation (i.e. variability) by up to 15% for mean kurtosis, 8% for bound pool fraction (BPF, myelin-sensitive), and 13% for T1, while enabling more efficient denoising of modalities limited in redundancy (e.g. relaxometry). In conclusion, multi-parametric spinal cord qMRI with unified readout is feasible and provides robust microstructural metrics with matched resolution and distortions, whose quality benefits from MP-PCA denoising, a useful pre-processing tool for spinal cord MRI.

neuroscience↗