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4. Learning the Sampling Pattern for MRI

Author

Sherry, Ferdia, Benning, Martin, Reyes, Juan Carlos De los, Graves, Martin J., Maierhofer, Georg, Williams, Guy, Schönlieb, Carola-Bibiane, and Ehrhardt, Matthias J.

Subjects
Electrical Engineering and Systems Science - Image and Video Processing, Computer Science - Computer Vision and Pattern Recognition, Mathematics - Numerical Analysis, Mathematics - Optimization and Control
Abstract

The discovery of the theory of compressed sensing brought the realisation that many inverse problems can be solved even when measurements are "incomplete". This is particularly interesting in magnetic resonance imaging (MRI), where long acquisition times can limit its use. In this work, we consider the problem of learning a sparse sampling pattern that can be used to optimally balance acquisition time versus quality of the reconstructed image. We use a supervised learning approach, making the assumption that our training data is representative enough of new data acquisitions. We demonstrate that this is indeed the case, even if the training data consists of just 7 training pairs of measurements and ground-truth images; with a training set of brain images of size 192 by 192, for instance, one of the learned patterns samples only 35% of k-space, however results in reconstructions with mean SSIM 0.914 on a test set of similar images. The proposed framework is general enough to learn arbitrary sampling patterns, including common patterns such as Cartesian, spiral and radial sampling., Comment: The main document is 12 pages, the supporting document is 2 pages and attached at the end of the main document

Published
2019

5. Multi-tasking to Correct: Motion-Compensated MRI via Joint Reconstruction and Registration

Author

Corona, Veronica, Aviles-Rivero, Angelica I., Debroux, Noemie, Graves, Martin, Guyader, Carole Le, Schoenlieb, Carola-Bibiane, and Williams, Guy

Subjects
Mathematics - Numerical Analysis
Abstract

This work addresses a central topic in Magnetic Resonance Imaging (MRI) which is the motion-correction problem in a joint reconstruction and registration framework. From a set of multiple MR acquisitions corrupted by motion, we aim at - jointly - reconstructing a single motion-free corrected image and retrieving the physiological dynamics through the deformation maps. To this purpose, we propose a novel variational model. First, we introduce an $L^2$ fidelity term, which intertwines reconstruction and registration along with the weighted total variation. Second, we introduce an additional regulariser which is based on the hyperelasticity principles to allow large and smooth deformations. We demonstrate through numerical results that this combination creates synergies in our complex variational approach resulting in higher quality reconstructions and a good estimate of the breathing dynamics. We also show that our joint model outperforms in terms of contrast, detail and blurring artefacts, a sequential approach., Comment: 12 pages, 3 figure, accepted for publication in Scale Space and Variational Methods in Computer Vision conference proceedings

Published
2019

6. Somatostatin Receptor PET/MR Imaging of Inflammation in Patients With Large Vessel Vasculitis and Atherosclerosis

Author

Ćorović, Andrej, Wall, Christopher, Nus, Meritxell, Gopalan, Deepa, Huang, Yuan, Imaz, Maria, Zulcinski, Michal, Peverelli, Marta, Uryga, Anna, Lambert, Jordi, Bressan, Dario, Maughan, Robert T., Pericleous, Charis, Dubash, Suraiya, Jordan, Natasha, Jayne, David R., Hoole, Stephen P., Calvert, Patrick A., Dean, Andrew F., Rassl, Doris, Barwick, Tara, Iles, Mark, Frontini, Mattia, Hannon, Greg, Manavaki, Roido, Fryer, Tim D., Aloj, Luigi, Graves, Martin J., Gilbert, Fiona J., Dweck, Marc R., Newby, David E., Fayad, Zahi A., Reynolds, Gary, Morgan, Ann W., Aboagye, Eric O., Davenport, Anthony P., Jørgensen, Helle F., Mallat, Ziad, Bennett, Martin R., Peters, James E., Rudd, James H.F., Mason, Justin C., and Tarkin, Jason M.

Published
2023
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7. Compressed Sensing Plus Motion (CS+M): A New Perspective for Improving Undersampled MR Image Reconstruction

Author

Aviles-Rivero, Angelica I., Debroux, Noémie, Williams, Guy, Graves, Martin J., and Schonlieb, Carola-Bibiane

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

We address the problem of reconstructing high quality images from undersampled MRI data. This is a challenging task due to the highly ill-posed nature of the problem. In particular, in dynamic MRI scans, the interaction between the target structure and the physical motion affects the acquired measurements leading to blurring artefacts and loss of fine details. In this work, we propose a framework for dynamic MRI reconstruction framed under a new multi-task optimisation model called Compressed Sensing Plus Motion (CS+M). Firstly, we propose a single optimisation problem that simultaneously computes the MRI reconstruction and the physical motion. Secondly, we show our model can be efficiently solved by breaking it up into two more computationally tractable problems. The potentials and generalisation capabilities of our approach are demonstrated in different clinical applications including cardiac cine, cardiac perfusion and brain perfusion imaging. We show, through numerical and graphical experiments, that the proposed scheme reduces blurring artefacts and preserves the target shape and fine details. We also report the highest quality reconstruction under highly undersampling rates in comparison to several state of the art techniques.

Published
2018

8. Spatial Encoding

Author

Buonincontri, Guido, Kaggie, Joshua, Graves, Martin, Buonincontri, Guido, Kaggie, Joshua, and Graves, Martin

Published
2020
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9. Conclusion

Author

Buonincontri, Guido, Kaggie, Joshua, Graves, Martin, Buonincontri, Guido, Kaggie, Joshua, and Graves, Martin

Published
2020
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10. Contrast Decoding

Author

Buonincontri, Guido, Kaggie, Joshua, Graves, Martin, Buonincontri, Guido, Kaggie, Joshua, and Graves, Martin

Published
2020
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11. Contrast Encoding

Author

Buonincontri, Guido, Kaggie, Joshua, Graves, Martin, Buonincontri, Guido, Kaggie, Joshua, and Graves, Martin

Published
2020
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12. Spatial Decoding

Author

Buonincontri, Guido, Kaggie, Joshua, Graves, Martin, Buonincontri, Guido, Kaggie, Joshua, and Graves, Martin

Published
2020
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13. Introduction

Author

Buonincontri, Guido, Kaggie, Joshua, Graves, Martin, Buonincontri, Guido, Kaggie, Joshua, and Graves, Martin

Published
2020
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16. Measuring cerebral enzymatic activity, brain pH and extracranial muscle metabolism with hyperpolarized 13C‐pyruvate.

Author

Khan, Alixander S., McLean, Mary A., Kaggie, Joshua D., Horvat‐Menih, Ines, Matys, Tomasz, Schulte, Rolf F., Locke, Matthew J., Grimmer, Ashley, Wodtke, Pascal, Latimer, Elizabeth, Frary, Amy, Graves, Martin J., and Gallagher, Ferdia A.

Subjects
MAGNETIC resonance imaging, CARBONIC anhydrase, PYRUVATE carboxylase, MUSCLE metabolism, ASPARTATE aminotransferase, BICARBONATE ions
Abstract

Hyperpolarized carbon‐13 (13C) magnetic resonance imaging (MRI) has shown promise for non‐invasive assessment of the cerebral metabolism of [1‐13C]pyruvate in both healthy volunteers and patients. The exchange of pyruvate to lactate catalysed by lactate dehydrogenase (LDH) and that of pyruvate flux to bicarbonate through pyruvate dehydrogenase (PDH) are the most widely studied reactions in vivo. Here we show the potential of the technique to probe additional enzymatic activity within the brain. Approximately 50 s after intravenous injection of hyperpolarized pyruvate, high‐flip‐angle pulses were used to detect cerebral 13C‐labelled carbon dioxide (13CO2), in addition to the 13C‐bicarbonate (H13CO3−) subsequently formed by carbonic anhydrase (CA). Brain pH measurements, which were weighted towards the extracellular compartment, were calculated from the ratio of H13CO3− to 13CO2 in seven volunteers using the Henderson–Hasselbalch equation, demonstrating an average pH ± SD of 7.40 ± 0.02, with inter‐observer reproducibility of 0.04. In addition, hyperpolarized [1‐13C]aspartate was also detected, demonstrating irreversible pyruvate carboxylation to oxaloacetate by pyruvate carboxylase (PC) and subsequent transamination by aspartate aminotransferase (AST), with the average flux being on average 11% ± 3% of that through PDH. A hyperpolarized [1‐13C]alanine signal was also detected, but this was localized to extracranial muscle tissue in keeping with skeletal alanine aminotransferase (ALT) activity. The results demonstrate the potential of hyperpolarized 13C‐MRI to assess cerebral and extracerebral [1‐13C]pyruvate metabolism in addition to LDH and PDH activity. Non‐invasive measurements of brain pH could be particularly important in assessing cerebral pathology given the wide range of disease processes that alter acid–base balance. [ABSTRACT FROM AUTHOR]

Published
2024
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17. Author Correction: Hyperpolarised 13C-MRI identifies the emergence of a glycolytic cell population within intermediate-risk human prostate cancer

Author

Sushentsev, Nikita, McLean, Mary A., Warren, Anne Y., Benjamin, Arnold J. V., Brodie, Cara, Frary, Amy, Gill, Andrew B., Jones, Julia, Kaggie, Joshua D., Lamb, Benjamin W., Locke, Matthew J., Miller, Jodi L., Mills, Ian G., Priest, Andrew N., Robb, Fraser J. L., Shah, Nimish, Schulte, Rolf F., Graves, Martin J., Gnanapragasam, Vincent J., Brindle, Kevin M., Barrett, Tristan, and Gallagher, Ferdia A.

Published
2022
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18. Hyperpolarised 13C-MRI identifies the emergence of a glycolytic cell population within intermediate-risk human prostate cancer

Author

Sushentsev, Nikita, McLean, Mary A., Warren, Anne Y., Benjamin, Arnold J. V., Brodie, Cara, Frary, Amy, Gill, Andrew B., Jones, Julia, Kaggie, Joshua D., Lamb, Benjamin W., Locke, Matthew J., Miller, Jodi L., Mills, Ian G., Priest, Andrew N., Robb, Fraser J. L., Shah, Nimish, Schulte, Rolf F., Graves, Martin J., Gnanapragasam, Vincent J., Brindle, Kevin M., Barrett, Tristan, and Gallagher, Ferdia A.

Published
2022
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20. Characterizing Diffusion from Microdialysis Catheters in the Human Brain: A Magnetic Resonance Imaging Study With Gadobutrol

Author

Stovell, Matthew G., primary, Ruetten, Pascal P.R., additional, Tozer, Daniel J., additional, Launey, Yoann, additional, Zimphango, Chisomo, additional, Thelin, Eric P., additional, Lupson, Victoria C., additional, Giorgi-Coll, Susan, additional, Carpenter, T. Adrian, additional, Mada, Marius O., additional, Jalloh, Ibrahim, additional, Helmy, Adel, additional, Wilson, Mark H., additional, Graves, Martin J., additional, Menon, David K., additional, Carpenter, Keri L.H., additional, and Hutchinson, Peter J., additional

Published
2024
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21. MINocyclinE to Reduce inflammation and blood‐brain barrier leakage in small Vessel diseAse (MINERVA): A phase II, randomized, double‐blind, placebo‐controlled experimental medicine trial

Author

Brown, Robin B., primary, Tozer, Daniel J., additional, Loubière, Laurence, additional, Harshfield, Eric L., additional, Hong, Young T., additional, Fryer, Tim D., additional, Williams, Guy B., additional, Graves, Martin J., additional, Aigbirhio, Franklin I., additional, O'Brien, John T., additional, and Markus, Hugh S., additional

Published
2024
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22. Imaging breast cancer using hyperpolarized carbon-13 MRI

Author

Gallagher, Ferdia A., Woitek, Ramona, McLean, Mary A., Gill, Andrew B., Garcia, Raquel Manzano, Provenzano, Elena, Riemer, Frank, Kaggie, Joshua, Chhabra, Anita, Ursprung, Stephan, Grist, James T., Daniels, Charlie J., Zaccagna, Fulvio, Laurent, Marie-Christine, Locke, Matthew, Hilborne, Sarah, Frary, Amy, Torheim, Turid, Boursnell, Chris, Schiller, Amy, Patterson, Ilse, Slough, Rhys, Carmo, Bruno, Kane, Justine, Biggs, Heather, Harrison, Emma, Deen, Surrin S., Patterson, Andrew, Lanz, Titus, Kingsbury, Zoya, Ross, Mark, Basu, Bristi, Baird, Richard, Lomas, David J., Sala, Evis, Wason, James, Rueda, Oscar M., Chin, Suet-Feung, Wilkinson, Ian B., Graves, Martin J., Abraham, Jean E., Gilbert, Fiona J., Caldas, Carlos, and Brindle, Kevin M.

Published
2020

23. A Modest Increase in 11C-PK11195-Positron Emission Tomography TSPO Binding in Depression Is Not Associated With Serum C-Reactive Protein or Body Mass Index

Author

Wlazly, Dominika, Dickinson, Amber, Foster, Andy, Knight, Clare, Leckey, Claire, Morgan, Paul, Morgan, Angharad, O'Hagan, Caroline, Touchard, Samuel, Khan, Shahid, Murphy, Phil, Parker, Christine, Patel, Jai, Richardson, Jill, Acton, Paul, Austin, Nigel, Bhattacharya, Anindya, Carruthers, Nick, de Boer, Peter, Drevets, Wayne, Isaac, John, Jones, Declan, Kemp, John, Kolb, Hartmuth, Nye, Jeff, Wittenberg, Gayle, Barker, Gareth, Bogdanova, Anna, Byrom, Heidi, Cash, Diana, Cattaneo, Annamaria, Enache, Daniela, Gee, Tony, Hastings, Caitlin, Kose, Melisa, Lombardo, Giulia, Mariani, Nicole, McLaughlin, Anna, Mondelli, Valeria, Nettis, Maria, Nikkheslat, Naghmeh, Pariante, Carmine, Randall, Karen, Schubert, Julia, Sforzini, Luca, Sheridan, Hannah, Simmons, Camilla, Singh, Nisha, Turkheimer, Federico, Van Loo, Vicky, Veronese, Mattia, Rodriguez, Marta Vicente, Wood, Toby, Worrell, Courtney, Zajkowska, Zuzanna, Campbell, Brian, Egebjerg, Jan, Eriksson, Hans, Gastambide, Francois, Adams, Karen Husted, Jeggo, Ross, Moeller, Thomas, Nelson, Bob, Plath, Niels, Thomsen, Christian, Pederson, Jan Torleif, Zorn, Stevin, Deith, Catherine, Farmer, Scott, McClean, John, McPherson, Andrew, Penandes, Nagore, Scouller, Paul, Sutherland, Murray, Attenburrow, Mary Jane, Benjamin, Jithen, Jones, Helen, Mada, Fran, Oladejo, Akintayo, Smith, Katy, Balice-Gordon, Rita, Binneman, Brendon, Duerr, James, Fullerton, Terence, Goli, Veeru, Hughes, Zoe, Piro, Justin, Samad, Tarek, Sporn, Jonathan, Hoskins, Liz, Kohn, Charmaine, Wilcock, Lauren, Aigbirhio, Franklin, Bhatti, Junaid, Bullmore, Ed, Chamberlain, Sam, Correia, Marta, Crofts, Anna, Fryer, Tim, Graves, Martin, Hatton, Alex, Kitzbichler, Manfred, Lynall, Mary-Ellen, Maurice, Christina, O'Donnell, Ciara, Pointon, Linda, St George Hyslop, Peter, Turner, Lorinda, Vertes, Petra, Widmer, Barry, Williams, Guy, Cavanagh, Jonathan, McColl, Alison, Shaw, Robin, Boddeke, Erik, Baird, Alison, Clare, Stuart, Cowen, Phil, Huang, I-Shu (Dante), Hurley, Sam, Lovestone, Simon, Nevado-Holgado, Alejo, Ribe, Elena, Vyas, Anviti, Winchester, Laura, Cleal, Madeleine, Gomez-Nicola, Diego, Mancuso, Renzo, Perry, Hugh, Cercignani, Mara, Clarke, Charlotte, Colasanti, Alessandro, Harrison, Neil, Murray, Rosemary, O'Connor, Jason, Mount, Howard, Schubert, Julia J., Fryer, Tim D., Manavaki, Roido, Kitzbichler, Manfred G., Nettis, Maria A., Pariante, Carmine M., Bullmore, Edward T., and Turkheimer, Federico E.

Published
2021
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27. Quantitative 23Na magnetic resonance imaging in the abdomen at 3 T.

Author

Birchall, Jonathan Richard, Horvat-Menih, Ines, Kaggie, Joshua Daniel, Riemer, Frank, Benjamin, Arnold Julian Vinoj, Graves, Martin John, Wilkinson, Ian, Gallagher, Ferdia Aidan, and McLean, Mary Anne

Subjects
VENA cava inferior, MAGNETIC resonance imaging, CEREBROSPINAL fluid, ABDOMEN, SPATIAL resolution
Abstract

Objectives: To assess the feasibility of sodium-23 MRI for performing quantitative and non-invasive measurements of total sodium concentration (TSC) and relaxation in a variety of abdominal organs. Materials and methods: Proton and sodium imaging of the abdomen was performed in 19 healthy volunteers using a 3D cones sequence and a sodium-tuned 4-rung transmit/receive body coil on a clinical 3 T system. The effects of B1 non-uniformity on TSC measurements were corrected using the double-angle method. The long-component of 23Na T2* relaxation time was measured using a series of variable echo-times. Results: The mean and standard deviation of TSC and long-component 23Na T2* values were calculated across the healthy volunteer group in the kidneys, cerebrospinal fluid (CSF), liver, gallbladder, spleen, aorta, and inferior vena cava. Discussion: Mean TSC values in the kidneys, liver, and spleen were similar to those reported using 23Na-MRI previously in the literature. Measurements in the CSF and gallbladder were lower, potentially due to the reduced spatial resolution achievable in a clinically acceptable scan time. Mean long-component 23Na T2* values were consistent with previous reports from the kidneys and CSF. Intra-population standard error was larger in smaller, fluid-filled structures due to fluid motion and partial volume effects. [ABSTRACT FROM AUTHOR]

Published
2024
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34. Quantifying normal human brain metabolism using hyperpolarized [1–13C]pyruvate and magnetic resonance imaging

Author

Grist, James T., McLean, Mary A., Riemer, Frank, Schulte, Rolf F., Deen, Surrin S., Zaccagna, Fulvio, Woitek, Ramona, Daniels, Charlie J., Kaggie, Joshua D., Matys, Tomasz, Patterson, Ilse, Slough, Rhys, Gill, Andrew B., Chhabra, Anita, Eichenberger, Rose, Laurent, Marie-Christine, Comment, Arnaud, Gillard, Jonathan H., Coles, Alasdair J., Tyler, Damian J., Wilkinson, Ian, Basu, Bristi, Lomas, David J., Graves, Martin J., Brindle, Kevin M., and Gallagher, Ferdia A.

Published
2019
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35. Sodium MRI with 3D-cones as a measure of tumour cellularity in high grade serous ovarian cancer

Author

Deen, Surrin S., Riemer, Frank, McLean, Mary A., Gill, Andrew B., Kaggie, Joshua D., Grist, James T., Crawford, Robin, Latimer, John, Baldwin, Peter, Earl, Helena M., Parkinson, Christine A., Smith, Sarah A., Hodgkin, Charlotte, Moore, Elizabeth, Jimenez-Linan, Mercedes, Brodie, Cara R., Addley, Helen C., Freeman, Susan J., Moyle, Penelope L., Sala, Evis, Graves, Martin J., Brenton, James D., and Gallagher, Ferdia A.

Published
2019
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36. Common Healthcare Related Instruments Subjected To Magnetic Attraction Study (CHRISTMAS): prospective in situ experimental study

Author

Ong, Shao J, primary, Chia, Koon Liang, additional, See, Teik Choon, additional, Graves, Martin, additional, Hoon, Desmond, additional, Hang, Joanne, additional, Teo, Lycia, additional, Su, Peijing, additional, Hallinan, James T P D, additional, Ong, Michael, additional, Ang, Bertrand, additional, and Quek, Swee Tian, additional

Published
2023
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44. Integrating Artificial Intelligence Tools in the Clinical Research Setting: The Ovarian Cancer Use Case

Author

Escudero Sanchez, Lorena, primary, Buddenkotte, Thomas, additional, Al Sa'd, Mohammad, additional, McCague, Cathal, additional, Darcy, James, additional, Rundo, Leonardo, additional, Samoshkin, Alex, additional, Graves, Martin, additional, Hollamby, Victoria, additional, Browne, Paul, additional, Crispin-Ortuzar, Mireia, additional, Woitek, Ramona, additional, Sala, Evis, additional, Schönlieb, Carola-Bibiane, additional, Doran, Simon, additional, and Öktem, Ozan, additional

Published
2023
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