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QSMxT: Robust Masking and Artefact Reduction for Quantitative Susceptibility Mapping [article]

Ashley Wilton Stewart, Simon Daniel Robinson, Kieran O'Brien, Jin Jin, Georg Widhalm, Gilbert Hangel, Angela Walls, Jonathan Goodwin, Korbinian Eckstein, Monique Tourell, Catherine Morgan, Aswin Narayanan (+2 others)
2021 bioRxiv   pre-print
AbstractPurposeQuantitative Susceptibility Mapping (QSM) is a post-processing technique applied to gradient-echo phase data.  ...  QSM algorithms require a signal mask to delineate regions with reliable phase signal for subsequent susceptibility estimation.  ...  Introduction Quantitative Susceptibility Mapping (QSM) is an MRI method that aims to calculate the magnetisation induced in tissues when placed in a magnetic field.  ... 
doi:10.1101/2021.05.05.442850 fatcat:upvjpxwhargdjh76utm4bsewvy

In Vivo Quantitative Susceptibility Mapping (QSM) in Alzheimer's Disease

Julio Acosta-Cabronero, Guy B. Williams, Arturo Cardenas-Blanco, Robert J. Arnold, Victoria Lupson, Peter J. Nestor, James R. Connor
2013 PLoS ONE  
Quantitative susceptibility mapping (QSM) has the potential to monitor in vivo iron levels by reconstructing magnetic susceptibility sources from field perturbations.  ...  Methods: In this context, the present study describes a complete methodological framework for magnetic susceptibility measurements with a review of its theoretical foundations.  ...  Acknowledgments We are grateful for the support from our patients and healthy volunteers. The authors are also extremely grateful to S.A. Sajjadi, K. Patterson and K.  ... 
doi:10.1371/journal.pone.0081093 pmid:24278382 pmcid:PMC3836742 fatcat:fgv5isdgyjhspavbq2iagoecfm

A Simulation Framework for Quantitative Validation of Artefact Correction in Diffusion MRI [chapter]

Mark S. Graham, Ivana Drobnjak, Hui Zhang
2015 Lecture Notes in Computer Science  
In this paper we demonstrate a simulation framework that enables the direct and quantitative comparison of post-processing methods for diffusion weighted magnetic resonance (DW-MR) images.  ...  Here we introduce a simulation framework that allows for the direct, quantitative assessment of techniques, enabling objective comparisons of existing and future methods.  ...  The simulation framework allowed us to quantitatively assess registration to b=0 as a method for correcting eddy currents.  ... 
doi:10.1007/978-3-319-19992-4_50 fatcat:66m76etrlbdsjk4zhpgg2r3nmm

An MR technique for simultaneous quantitative imaging of water content, conductivity and susceptibility, with application to brain tumours using a 3T hybrid MR-PET scanner

Yupeng Liao, Ana-Maria Oros-Peusquens, Johannes Lindemeyer, Nazim Lechea, Carolin Weiß -Lucas, Karl-Josef Langen, N. Jon Shah
2019 Scientific Reports  
The purpose of this study is to develop a method for simultaneously acquiring quantitative water content, electrical conductivity and susceptibility maps based on a 2D multi-echo gradient echo sequence  ...  Approaches for the quantitative mapping of water content, electrical conductivity and susceptibility have been developed independently.  ...  Acknowledgements The authors would like to thank Dr. G. Stoffels and Dr. C. Filss for the support in hybrid MR-PET for measurements and Ms. Claire Rick for proof reading the manuscript.  ... 
doi:10.1038/s41598-018-36435-8 pmid:30643159 pmcid:PMC6331621 fatcat:5qplvfynrjgcdg4xtcgcaozw74

A Comprehensive Framework for the Detection of Individual Brain Perfusion Abnormalities Using Arterial Spin Labeling [chapter]

Camille Maumet, Pierre Maurel, Jean-Christophe Ferré, Christian Barillot
2012 Lecture Notes in Computer Science  
In this paper, we introduce a new framework to automatically outline patterns of abnormal perfusion in individual patients by means of an ASL template.  ...  We compare two models of normal perfusion and assess the quality of detections comparing an a contrario approach to the Generalized Linear Model (GLM).  ...  Conclusion We have presented a comprehensive framework for the detection of brain perfusion abnormalities in individual patients by comparison to a template of healthy subjects.  ... 
doi:10.1007/978-3-642-33454-2_67 fatcat:ijorjj6cnza7vbfdtxkgabspdu

A robust multi-scale approach to quantitative susceptibility mapping

Julio Acosta-Cabronero, Carlos Milovic, Hendrik Mattern, Cristian Tejos, Oliver Speck, Martina F. Callaghan
2018 NeuroImage  
A B S T R A C T Quantitative Susceptibility Mapping (QSM), best known as a surrogate for tissue iron content, is becoming a highly relevant MRI contrast for monitoring cellular and vascular status in aging  ...  ) for Macroscopic-Vessel Suppressed Susceptibility Mapping (MVSSM), and (iv) high spatial specificity and definition for HPSM-based Susceptibility-Weighted Imaging (HPSM-SWI) and related intensity projections  ...  We thank the EUFIND consortium (funded by the EU Joint Programme -Neurodegenerative Disease Research, JPND) for contributing to this study with a 7 Tesla MRI dataset.  ... 
doi:10.1016/j.neuroimage.2018.07.065 pmid:30075277 pmcid:PMC6215336 fatcat:hna4wale2zdmfmszsii2vbwthe

High-resolution characterisation of the aging brain using simultaneous quantitative susceptibility mapping (QSM) and R 2 * measurements at 7 T

Matthew J. Betts, Julio Acosta-Cabronero, Arturo Cardenas-Blanco, Peter J. Nestor, Emrah Düzel
2016 NeuroImage  
Quantitative susceptibility mapping (QSM) has recently emerged as a novel magnetic resonance imaging (MRI) method to detect non-haem iron deposition, calcifications, demyelination and vascular lesions  ...  The present study, therefore, demonstrated that in vivo QSM using ultra-high field MRI provides a novel means to characterize age-related differences in the human brain, but also combining QSM and R2*  ...  Recently, a novel technique termed quantitative susceptibility mapping (QSM) has been proposed to try to overcome the non-locality of magnetic field fluctuations.  ... 
doi:10.1016/j.neuroimage.2016.05.024 pmid:27181761 fatcat:fupj23xazjbl7kmqkzzwkz2a4m

A 3D two-point method for whole-brain water content and relaxation time mapping: Comparison with gold standard methods

Melissa Schall, Markus Zimmermann, Elene Iordanishvili, Yun Gu, N. Jon Shah, Ana-Maria Oros-Peusquens, Quan Jiang
2018 PLoS ONE  
Quantitative imaging of the human brain is of great interest in clinical research as it enables the identification of a range of MR biomarkers useful in diagnosis, treatment and prognosis of a wide spectrum  ...  For H 2 O and T 2 * mapping, the 3D two-point results were compared to a measurement conducted with a multiple-echo GRE with long TR and T 1 is compared to results from a Look-Locker method, TAPIR.  ...  Zaheer Abbas for the helpful and consequential discussions about water content normalisation and to Claire Rick for proofreading.  ... 
doi:10.1371/journal.pone.0201013 pmid:30161125 fatcat:4arxag722faqzlkdwaggqmidsy

Multi-channel Registration for Diffusion MRI: Longitudinal Analysis for the Neonatal Brain [chapter]

Alena Uus, Maximilian Pietsch, Irina Grigorescu, Daan Christiaens, Jacques-Donald Tournier, Lucilio Cordero Grande, Jana Hutter, David Edwards, Joseph Hajnal, Maria Deprez
2020 Lecture Notes in Computer Science  
In this work, we extend the pipeline for registration of multi-shell high angular resolution diffusion imaging (HARDI) [15] with a novel similarity metric based on angular correlation and an option for  ...  The contributions of channels to the displacement field are weighted with spatially varying certainty maps. The implementation is based on MRtrix3 (MRtrix3: toolbox.  ...  In this work we present a framework for multi-channel brain registration that allows local certainty-based fusion of dMRI-derived ODFs and structural MRI and is based on a novel similarity metric for dMRI  ... 
doi:10.1007/978-3-030-50120-4_11 fatcat:w7zbxujkgzar7jqzldgtcilbde

Realistic simulation of artefacts in diffusion MRI for validating post-processing correction techniques

Mark S. Graham, Ivana Drobnjak, Hui Zhang
2016 NeuroImage  
In this paper we demonstrate a simulation framework that enables the direct and quantitative comparison of post-processing methods for diffusion weighted magnetic resonance (DW-MR) images.  ...  Here we introduce a simulation framework that allows for the direct, quantitative assessment of techniques, enabling objective comparisons of existing and future methods.  ...  Acknowledgments We would like to thank Jesper Andersson for providing us with a version of eddy that outputs displacement fields, and for helpful discussions.  ... 
doi:10.1016/j.neuroimage.2015.11.006 pmid:26549300 fatcat:iuyrfh5mbzg6rgavqin3rhcvsy

A streamlined acquisition for mapping baseline brain oxygenation using quantitative BOLD

Alan J. Stone, Nicholas P. Blockley
2017 NeuroImage  
Here we propose a refinement of the qBOLD methodology, dubbed streamlined-qBOLD, in order to provide a clinically feasible method for mapping baseline brain oxygenation.  ...  A B S T R A C T Quantitative BOLD (qBOLD) is a non-invasive MR technique capable of producing quantitative measurements of the haemodynamic and metabolic properties of the brain.  ...  Introduction Techniques capable of providing quantitative maps of baseline brain oxygenation provide valuable information about the metabolic profile of brain tissue and have clinical applications in diseases  ... 
doi:10.1016/j.neuroimage.2016.11.057 pmid:27915118 fatcat:2vxvknxuzrc27cqnpg4n7pgfhi

hMRI – A toolbox for quantitative MRI in neuroscience and clinical research

Karsten Tabelow, Evelyne Balteau, John Ashburner, Martina F. Callaghan, Bogdan Draganski, Gunther Helms, Ferath Kherif, Tobias Leutritz, Antoine Lutti, Christophe Phillips, Enrico Reimer, Lars Ruthotto (+4 others)
2019 NeuroImage  
Neuroscience and clinical researchers are increasingly interested in quantitative magnetic resonance imaging (qMRI) due to its sensitivity to micro-structural properties of brain tissue such as axon, myelin  ...  ) that can be used for quantitative parameter analysis and accurate delineation of subcortical brain structures.  ...  susceptibility mapping/weighted imaging approaches.  ... 
doi:10.1016/j.neuroimage.2019.01.029 pmid:30677501 pmcid:PMC6547054 fatcat:6m7s4t2vajhshgybudevhuh3bi

The Digital Brain Bank: an open access platform for post-mortem datasets [article]

Benjamin C. Tendler, Taylor Hanayik, Olaf Ansorge, Sarah Bangerter-Christensen, Gregory S. Berns, Mads F. Bertelsen, Katherine L. Bryant, Sean Foxley, Amy F.D. Howard, Istvan Huszar, Alexandre A. Khrapitchev, Anna Leonte (+14 others)
2021 bioRxiv   pre-print
Taken together, the Digital Brain Bank provides a cross-scale, cross-species investigation framework facilitating the incorporation of post-mortem data into neuroimaging studies.  ...  Post-mortem MRI provides the opportunity to acquire high-resolution datasets to investigate neuroanatomy, and validate the origins of image contrast through microscopy comparisons.  ...  The Wellcome Centre for Integrative Neuroimaging is supported by core funding from the Wellcome Trust (203139/Z/16/Z).  ... 
doi:10.1101/2021.06.21.449154 fatcat:fyg645rmojea7hpa2sscyku4cq

Tissue-type mapping of gliomas

Felix Raschke, Thomas R. Barrick, Timothy L. Jones, Guang Yang, Xujiong Ye, Franklyn A. Howe
2019 NeuroImage: Clinical  
To develop a statistical method of combining multimodal MRI (mMRI) of adult glial brain tumours to generate tissue heterogeneity maps that indicate tumour grade and infiltration margins.  ...  Image intensity normalisation using histogram matching was applied across the entire dataset of T2w and PDw images to enable semi-quantitative comparisons of T2w and PDw images between patients (Verma  ...  the p, q, T2n, and PDn images only, as a precursor to fully quantitative T2 and PD acquisitions in future studies.  ... 
doi:10.1016/j.nicl.2018.101648 pmid:30630760 pmcid:PMC6411966 fatcat:ilvqlrjl7vdi3ahmfasg4ukgvm

A multi-contrast MRI approach to thalamus segmentation [article]

Veronica Corona, Jan Lellmann, Peter Nestor, Carola-Bibiane Schoenlieb, Julio Acosta-Cabronero
2018 arXiv   pre-print
susceptibility mapping (QSM) information.  ...  Routine interventions to improve symptom severity in movement disorders, for example, often consist of surgery or deep brain stimulation to diencephalic nuclei.  ...  Moreover, CBS is thankful for support by the Alan Turing Institute.  ... 
arXiv:1807.10757v1 fatcat:ydgmgwmuh5huvfoan2o3jjxjai
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