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Bayesian Inference for Non-linear forward model by using a VAE-based neural network structure (2024)
Journal Article
Zhang, Y., Zheng, J., & Chappell, M. (2024). Bayesian Inference for Non-linear forward model by using a VAE-based neural network structure. IEEE Transactions on Signal Processing, 72, 1400-1411. https://doi.org/10.1109/tsp.2024.3374115

In this paper, a Variational Autoencoder (VAE) based framework is introduced to solve parameter estimation problems for non-linear forward models. In particular, we focus on applications in the field of medical imaging where many thousands of model-b... Read More about Bayesian Inference for Non-linear forward model by using a VAE-based neural network structure.

BASIL: A Toolbox for Perfusion Quantification using Arterial Spin Labelling (2023)
Journal Article
Chappell, M. A., Kirk, T. F., Craig, M. S., McConnell, F. A. K., Zhao, M. Y., MacIntosh, B. J., …Woolrich, M. W. (2023). BASIL: A Toolbox for Perfusion Quantification using Arterial Spin Labelling. Imaging Neuroscience, https://doi.org/10.1162/imag_a_00041

Arterial Spin Labelling (ASL) MRI is now an established non-invasive method to quantify cerebral blood flow and is increasingly being used in a variety of neuroimaging applications. With standard ASL acquisition protocols widely available, there is a... Read More about BASIL: A Toolbox for Perfusion Quantification using Arterial Spin Labelling.

Unified Surface and Volumetric Inference on Functional Imaging Data (2023)
Conference Proceeding
Kirk, T. F., Craig, M. S., & Chappell, M. A. (2023). Unified Surface and Volumetric Inference on Functional Imaging Data. In J. Duncan, H. Greenspan, A. Madabhushi, P. Mousavi, S. Salcudean, T. Syeda-Mahmood, & R. Taylor (Eds.), Medical Image Computing and Computer Assisted Intervention – MICCAI 2023: 26th International Conference, Vancouver, BC, Canada, October 8–12, 2023, Proceedings, Part VIII (399-408). https://doi.org/10.1007/978-3-031-43993-3_39

Surface-based analysis methods for functional imaging data have been shown to offer substantial benefits for the study of the human cortex, namely in the localisation of functional areas and the establishment of inter-subject correspondence. A new ap... Read More about Unified Surface and Volumetric Inference on Functional Imaging Data.

Brain perfusion imaging by multi‐delay arterial spin labeling: Impact of modeling dispersion and interaction with denoising strategies and pathology (2023)
Journal Article
Pires Monteiro, S., Pinto, J., Chappell, M. A., Fouto, A., Baptista, M. V., Vilela, P., & Figueiredo, P. (2023). Brain perfusion imaging by multi‐delay arterial spin labeling: Impact of modeling dispersion and interaction with denoising strategies and pathology. Magnetic Resonance in Medicine, 90(5), 1889-1904. https://doi.org/10.1002/mrm.29783

Purpose: Arterial spin labeling (ASL) acquisitions at multiple post-labeling delays may provide more accurate quantification of cerebral blood flow (CBF), by fitting appropriate kinetic models and simultaneously estimating relevant parameters such as... Read More about Brain perfusion imaging by multi‐delay arterial spin labeling: Impact of modeling dispersion and interaction with denoising strategies and pathology.

MRI assessment of cerebral perfusion in clinical trials (2023)
Journal Article
Wang, X., Bishop, C., O'Callaghan, J., Gayhoor, A., Albani, J., Theriault, W., …Becerra, L. (2023). MRI assessment of cerebral perfusion in clinical trials. Drug Discovery Today, 28(4), Article 103506. https://doi.org/10.1016/j.drudis.2023.103506

Neurodegenerative mechanisms affect the brain through a variety of processes that are reflected as changes in brain structure and physiology. Although some biomarkers for these changes are well established, others are at different stages of developme... Read More about MRI assessment of cerebral perfusion in clinical trials.

Time-encoded pseudo-continuous arterial spin labeling: Increasing SNR in ASL dynamic angiography (2022)
Journal Article
Woods, J. G., Schauman, S. S., Chiew, M., Chappell, M. A., & Okell, T. W. (2023). Time-encoded pseudo-continuous arterial spin labeling: Increasing SNR in ASL dynamic angiography. Magnetic Resonance in Medicine, 89(4), 1323-1341. https://doi.org/10.1002/mrm.29491

Purpose: Dynamic angiography using arterial spin labeling (ASL) can provide detailed hemodynamic information. However, the long time-resolved readouts require small flip angles to preserve ASL signal for later timepoints, limiting SNR. By using time-... Read More about Time-encoded pseudo-continuous arterial spin labeling: Increasing SNR in ASL dynamic angiography.

Potential Diagnostic Applications of Multi-Delay Arterial Spin Labeling in Early Alzheimer’s Disease: The Chinese Imaging, Biomarkers, and Lifestyle Study (2022)
Journal Article
Sun, M., Wang, Y. L., Li, R., Jiang, J., Zhang, Y., Li, W., …Xu, J. (2022). Potential Diagnostic Applications of Multi-Delay Arterial Spin Labeling in Early Alzheimer’s Disease: The Chinese Imaging, Biomarkers, and Lifestyle Study. Frontiers in Neuroscience, 16, Article 934471. https://doi.org/10.3389/fnins.2022.934471

Background: Cerebral blood flow (CBF) alterations are involved in the onset and progression of Alzheimer’s disease (AD) and can be a potential biomarker. However, CBF measured by single-delay arterial spin labeling (ASL) for discrimination of mild co... Read More about Potential Diagnostic Applications of Multi-Delay Arterial Spin Labeling in Early Alzheimer’s Disease: The Chinese Imaging, Biomarkers, and Lifestyle Study.

Review and consensus recommendations on clinical APT-weighted imaging approaches at 3T: Application to brain tumors (2022)
Journal Article
Zhou, J., Zaiss, M., Knutsson, L., Sun, P. Z., Ahn, S. S., Aime, S., …Zijl, P. C. M. (2022). Review and consensus recommendations on clinical APT-weighted imaging approaches at 3T: Application to brain tumors. Magnetic Resonance in Medicine, 88(2), 546-574. https://doi.org/10.1002/mrm.29241

Amide proton transfer-weighted (APTw) MR imaging shows promise as a biomarker of brain tumor status. Currently used APTw MRI pulse sequences and protocols vary substantially among different institutes, and there are no agreed-on standards in the imag... Read More about Review and consensus recommendations on clinical APT-weighted imaging approaches at 3T: Application to brain tumors.

Amide proton transfer imaging in stroke (2022)
Journal Article
Heo, H. Y., Tee, Y. K., Harston, G., Leigh, R., & Chappell, M. A. (2022). Amide proton transfer imaging in stroke. NMR in Biomedicine, Article e4734. https://doi.org/10.1002/nbm.4734

Amide proton transfer (APT) imaging, a variant of chemical exchange saturation transfer MRI, has shown promise in detecting ischemic tissue acidosis following impaired aerobic metabolism in animal models and in human stroke patients due to the sensit... Read More about Amide proton transfer imaging in stroke.

Quantitative chemical exchange saturation transfer imaging of nuclear overhauser effects in acute ischemic stroke (2022)
Journal Article
Msayib, Y., Harston, G. W., Ray, K. J., Larkin, J. R., Sutherland, B. A., Sheerin, F., …Chappell, M. A. (2022). Quantitative chemical exchange saturation transfer imaging of nuclear overhauser effects in acute ischemic stroke. Magnetic Resonance in Medicine, 88(1), 341-356. https://doi.org/10.1002/mrm.29187

Purpose: In chemical exchange saturation transfer imaging, saturation effects between (Formula presented.) 2 to (Formula presented.) 5 ppm (nuclear Overhauser effects, NOEs) have been shown to exhibit contrast in preclinical stroke models. Our previo... Read More about Quantitative chemical exchange saturation transfer imaging of nuclear overhauser effects in acute ischemic stroke.

Validation of the estimation of the macrovascular contribution in multi‐timepoint arterial spin labeling MRI using a 2‐component kinetic model (2021)
Journal Article
Plas, M. C. E., Craig, M., Schmid, S., Chappell, M. A., & Osch, M. J. P. (2022). Validation of the estimation of the macrovascular contribution in multi‐timepoint arterial spin labeling MRI using a 2‐component kinetic model. Magnetic Resonance in Medicine, 87(1), 85-101. https://doi.org/10.1002/mrm.28960

Purpose In this paper, the ability to quantify cerebral blood flow by arterial spin labeling (ASL) was studied by investigating the separation of the macrovascular and tissue component using a 2-component model. Underlying assumptions of this model,... Read More about Validation of the estimation of the macrovascular contribution in multi‐timepoint arterial spin labeling MRI using a 2‐component kinetic model.

Partial volume correction in arterial spin labeling perfusion MRI: A method to disentangle anatomy from physiology or an analysis step too far? (2021)
Journal Article
Chappell, M. A., McConnell, F. A. K., Golay, X., Günther, M., Hernandez-Tamames, J. A., van Osch, M. J., & Asllani, I. (2021). Partial volume correction in arterial spin labeling perfusion MRI: A method to disentangle anatomy from physiology or an analysis step too far?. NeuroImage, 238, Article 118236. https://doi.org/10.1016/j.neuroimage.2021.118236

The mismatch in the spatial resolution of Arterial Spin Labeling (ASL) MRI perfusion images and the anatomy of functionally distinct tissues in the brain leads to a partial volume effect (PVE), which in turn confounds the estimation of perfusion into... Read More about Partial volume correction in arterial spin labeling perfusion MRI: A method to disentangle anatomy from physiology or an analysis step too far?.

Examination of optimized protocols for pCASL: Sensitivity to macrovascular contamination, flow dispersion, and prolonged arterial transit time (2021)
Journal Article
Zhang, L. X., Woods, J. G., Okell, T. W., & Chappell, M. A. (2021). Examination of optimized protocols for pCASL: Sensitivity to macrovascular contamination, flow dispersion, and prolonged arterial transit time. Magnetic Resonance in Medicine, 86(4), 2208-2219. https://doi.org/10.1002/mrm.28839

Purpose Previously, multi- post-labeling delays (PLD) pseudo-continuous arterial spin labeling (pCASL) protocols have been optimized for the estimation accuracy of the cerebral blood flow (CBF) with/without the arterial transit time (ATT) under a st... Read More about Examination of optimized protocols for pCASL: Sensitivity to macrovascular contamination, flow dispersion, and prolonged arterial transit time.

Study Protocol: The Heart and Brain Study (2021)
Journal Article
Suri, S., Bulte, D., Chiesa, S. T., Ebmeier, K. P., Jezzard, P., Rieger, S. W., …Mackay, C. E. (2021). Study Protocol: The Heart and Brain Study. Frontiers in Physiology, 12, Article 643725. https://doi.org/10.3389/fphys.2021.643725

Background: It is well-established that what is good for the heart is good for the brain. Vascular factors such as hypertension, diabetes, and high cholesterol, and genetic factors such as the apolipoprotein E4 allele increase the risk of developing... Read More about Study Protocol: The Heart and Brain Study.

Age-related normative changes in cerebral perfusion: data from The Irish Longitudinal Study on Ageing (TILDA) (2021)
Journal Article
Ní Leidhin, C., McMorrow, J., Carey, D., Newman, L., Williamson, W., Fagan, A. J., …Knight, S. P. (2021). Age-related normative changes in cerebral perfusion: data from The Irish Longitudinal Study on Ageing (TILDA). NeuroImage, 229, Article 117741. https://doi.org/10.1016/j.neuroimage.2021.117741

Objective To establish normative reference values for total grey matter cerebral blood flow (CBFGM) measured using pseudo-continuous arterial spin labelling (pCASL) MRI in a large cohort of community-dwelling adults aged 54 years and older. Backgroun... Read More about Age-related normative changes in cerebral perfusion: data from The Irish Longitudinal Study on Ageing (TILDA).

Designing and comparing optimized pseudo-continuous Arterial Spin Labeling protocols for measurement of cerebral blood flow (2020)
Journal Article
Woods, J. G., Chappell, M. A., & Okell, T. W. (2020). Designing and comparing optimized pseudo-continuous Arterial Spin Labeling protocols for measurement of cerebral blood flow. NeuroImage, 223, Article 117246. https://doi.org/10.1016/j.neuroimage.2020.117246

Arterial Spin Labeling (ASL) is a non-invasive, non-contrast, perfusion imaging technique which is inherently SNR limited. It is, therefore, important to carefully design scan protocols to ensure accurate measurements. Many pseudo-continuous ASL (PCA... Read More about Designing and comparing optimized pseudo-continuous Arterial Spin Labeling protocols for measurement of cerebral blood flow.

Does the magnetization transfer effect bias chemical exchange saturation transfer effects? Quantifying chemical exchange saturation transfer in the presence of magnetization transfer (2020)
Journal Article
Smith, A. K., Ray, K. J., Larkin, J. R., Craig, M., Smith, S. A., & Chappell, M. A. (2020). Does the magnetization transfer effect bias chemical exchange saturation transfer effects? Quantifying chemical exchange saturation transfer in the presence of magnetization transfer. Magnetic Resonance in Medicine, 84(3), 1359-1375. https://doi.org/10.1002/mrm.28212

ExploreASL: an image processing pipeline for multi-center ASL perfusion MRI studies (2019)
Working Paper
Mutsaerts, H., Petr, J., Groot, P., Vandemaele, P., Ingala, S., Robertson, A. D., …Barkhof, F. ExploreASL: an image processing pipeline for multi-center ASL perfusion MRI studies

Arterial spin labeling (ASL) has undergone significant development since its inception, with a focus on improving standardization and reproducibility of its acquisition and quantification. In a community-wide effort towards robust and reproducible cl... Read More about ExploreASL: an image processing pipeline for multi-center ASL perfusion MRI studies.

Toblerone: Surface-Based Partial Volume Estimation (2019)
Journal Article
Kirk, T. F., Coalson, T. S., Craig, M. S., & Chappell, M. A. (2020). Toblerone: Surface-Based Partial Volume Estimation. IEEE Transactions on Medical Imaging, 39(5), 1501-1510. https://doi.org/10.1109/tmi.2019.2951080

Partial volume effects (PVE) present a source of confound for the analysis of functional imaging data. Correction for PVE requires estimates of the partial volumes (PVs) present in an image. These estimates are conventionally obtained via volumetric... Read More about Toblerone: Surface-Based Partial Volume Estimation.

Calibration of arterial spin labeling data—potential pitfalls in post‐processing (2019)
Journal Article
Pinto, J., Chappell, M. A., Okell, T. W., Mezue, M., Segerdahl, A. R., Tracey, I., …Figueiredo, P. (2020). Calibration of arterial spin labeling data—potential pitfalls in post‐processing. Magnetic Resonance in Medicine, 83(4), 1222-1234. https://doi.org/10.1002/mrm.28000

Purpose To assess the impact of the different post?processing options in the calibration of arterial spin labeling (ASL) data on perfusion quantification and its reproducibility. Theory and Methods Absolute quantification of perfusion measuremen... Read More about Calibration of arterial spin labeling data—potential pitfalls in post‐processing.