Francesco Grussu, Stefano B. Blumberg, Marco Battiston, Lebina S. Kakkar, Hongxiang Lin, Andrada Ianuş, Torben Schneider, Saurabh Singh, Roger Bourne, Shonit Punwani, David Atkinson, Claudia A. M. Gandini Wheeler-Kingshott, Eleftheria Panagiotaki, Thomy Mertzanidou, Daniel C. Alexander, Institut Català de la Salut, [Grussu F] Queen Square MS Centre, Queen Square Institute of Neurology, Faculty of Brain Sciences, University College London, London, United Kingdom. Centre for Medical Image Computing, Department of Computer Science, University College London, London, United Kingdom. Radiomics Group, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain. [Blumberg SB] Centre for Medical Image Computing, Department of Computer Science, University College London, London, United Kingdom. [Battiston M] Queen Square MS Centre, Queen Square Institute of Neurology, Faculty of Brain Sciences, University College London, London, United Kingdom. [Kakkar LS] Centre for Medical Imaging, University College London, London, United Kingdom. [Lin H] Centre for Medical Image Computing, Department of Computer Science, University College London, London, United Kingdom. [Ianuş A] Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, Portugal, and Vall d'Hebron Barcelona Hospital Campus
Brain; Protocol design; Quantitative MRI (qMRI) Cerebro; Diseño de protocolo; Resonancia magnética cuantitativa (qMRI) Cervell; Disseny del protocol; Ressonància magnètica quantitativa (qMRI) Purpose: We investigate the feasibility of data-driven, model-free quantitative MRI (qMRI) protocol design on in vivo brain and prostate diffusion-relaxation imaging (DRI). Methods: We select subsets of measurements within lengthy pilot scans, without identifying tissue parameters for which to optimise for. We use the “select and retrieve via direct upsampling” (SARDU-Net) algorithm, made of a selector, identifying measurement subsets, and a predictor, estimating fully-sampled signals from the subsets. We implement both using artificial neural networks, which are trained jointly end-to-end. We deploy the algorithm on brain (32 diffusion-/T1-weightings) and prostate (16 diffusion-/T2-weightings) DRI scans acquired on three healthy volunteers on two separate 3T Philips systems each. We used SARDU-Net to identify sub-protocols of fixed size, assessing reproducibility and testing sub-protocols for their potential to inform multi-contrast analyses via the T1-weighted spherical mean diffusion tensor (T1-SMDT, brain) and hybrid multi-dimensional MRI (HM-MRI, prostate) models, for which sub-protocol selection was not optimised explicitly. Results: In both brain and prostate, SARDU-Net identifies sub-protocols that maximise information content in a reproducible manner across training instantiations using a small number of pilot scans. The sub-protocols support T1-SMDT and HM-MRI multi-contrast modelling for which they were not optimised explicitly, providing signal quality-of-fit in the top 5% against extensive sub-protocol comparisons. Conclusions: Identifying economical but informative qMRI protocols from subsets of rich pilot scans is feasible and potentially useful in acquisition-time-sensitive applications in which there is not a qMRI model of choice. SARDU-Net is demonstrated to be a robust algorithm for data-driven, model-free protocol design. This project was funded by the Engineering and Physical Sciences Research Council (EPSRC EP/R006032/1, M020533/1, G007748, I027084, N018702). This project has received funding under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 634541 and 666992, and from: Rosetrees Trust (United Kingdom, funding FG); Prostate Cancer United Kingdom Targeted Call 2014 (Translational Research St.2, project reference PG14-018-TR2); Cancer Research United Kingdom grant ref. A21099; Spinal Research (United Kingdom), Wings for Life (Austria), Craig H. Neilsen Foundation (United States) for jointly funding the INSPIRED study; Wings for Life (#169111); United Kingdom Multiple Sclerosis Society (grants 892/08 and 77/2017); the Department of Health’s National Institute for Health Research (NIHR) Biomedical Research Centres and UCLH NIHR Biomedical Research Centre; Champalimaud Centre for the Unknown, Lisbon (Portugal); European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 101003390. FG is currently supported by the investigator-initiated PREdICT study at the Vall d’Hebron Institute of Oncology (Barcelona), funded by AstraZeneca and CRIS Cancer Foundation.