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MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation [article]

J-Donald Tournier, Robert E Smith, David A Raffelt, Rami Tabbara, Thijs Dhollander, Maximilian Pietsch, Daan Christiaens, Ben Jeurissen, Chun-Hung Yeh, Alan Connelly
2019 bioRxiv   pre-print
MRtrix3 is an open-source, cross-platform software package for medical image processing, analysis and visualization, with a particular emphasis on the investigation of the brain using diffusion MRI.  ...  It is implemented using a fast, modular and flexible general-purpose code framework for image data access and manipulation, enabling efficient development of new applications, whilst retaining high computational  ...  Acknowledgements This work was primarily supported by the National Health and Medical Research Council (NHMRC) of Australia (Program Grants 400121, 628952, 1091593; AC research fellowship 1026077).  ... 
doi:10.1101/551739 fatcat:eivbgdbepfefvipaavt64umloe

MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation

J-Donald Tournier, Robert Smith, David Raffelt, Rami Tabbara, Thijs Dhollander, Maximilian Pietsch, Daan Christiaens, Ben Jeurissen, Chun-Hung Yeh, Alan Connelly
2019 NeuroImage  
MRtrix3 is an open-source, cross-platform software package for medical image processing, analysis and visualisation, with a particular emphasis on the investigation of the brain using diffusion MRI.  ...  It is implemented using a fast, modular and flexible general-purpose code framework for image data access and manipulation, enabling efficient development of new applications, whilst retaining high computational  ...  MRtrix3 has been designed as an open-source, modular software platform for medical image analysis and visualization.  ... 
doi:10.1016/j.neuroimage.2019.116137 pmid:31473352 fatcat:66gp2lhzzbhs5ikeidmjx2k27q

Diffusion Kurtosis Imaging of the neonatal Spinal Cord: design and application of the first processing pipeline implemented in Spinal Cord Toolbox [article]

Rosella Denise Tro', Monica Roascio, Domenico Tortora, Mariasavina Severino, Andrea Rossi, Julien Cohen-Adad, Marco Massimo Fato, Gabriele Arnulfo
2021 medRxiv   pre-print
Diffusion Kurtosis Imaging (DKI) has undisputed advantages over more classical diffusion Magnetic Resonance Imaging (dMRI), as witnessed by a fast-increasing number of clinical applications and software  ...  of processing algorithms customized for adult SC.  ...  ), University of Genoa, Italy) and the LIFT (Laboratorio di Imaging Funzionale 3 Tesla).  ... 
doi:10.1101/2021.03.12.21253413 fatcat:yaytyxwblnfvzht5shsqjaxcey

Brain Modelling as a Service: The Virtual Brain on EBRAINS [article]

Michael Schirner, Lia Domide, Dionysios Perdikis, Paul Triebkorn, Leon Stefanovski, Roopa Pai, Paula Popa, Bogdan Valean, Jessica Palmer, Chloê Langford, André Blickensdörfer, Michiel van der Vlag (+32 others)
2021 arXiv   pre-print
It offers services for constructing, simulating and analysing brain network models (BNMs) including the TVB network simulator; magnetic resonance imaging (MRI) processing pipelines to extract structural  ...  The Virtual Brain (TVB) is now available as open-source cloud ecosystem on EBRAINS, a shared digital research platform for brain science.  ...  on the Supercomputer PizDaint of the Fenix Infrastructure (projects ich10, ich12) and  ... 
arXiv:2102.05888v2 fatcat:gjlrpzszj5c23eu53o44wx5lxa

Multi-Tissue Multi-Compartment models of diffusion MRI [article]

Matteo Frigo, Rutger H.J. Fick, Mauro Zucchelli, Samuel Deslauriers-Gauthier, Rachid Deriche
2021 bioRxiv   pre-print
We show how modelling multiple tissues provides a new interpretation of the concepts of signal fraction and volume fraction in the context of multi-compartment modelling.  ...  In this work we propose a novel multi-tissue formulation of classical multi-compartment models that relies on more common single-TE acquisitions and can be employed in the analysis of previously acquired  ...  Yeh, and A. Connelly. Mrtrix3: A fast, flexible and open software framework for medical image processing and visualisation. NeuroImage, 202:116137, 2019. D. C. Van Essen, K. Ugurbil, E.  ... 
doi:10.1101/2021.01.29.428843 fatcat:azuyx5xdnzenvkgtvfcgtd4vje

Processing the diffusion-weighted magnetic resonance imaging of the PING dataset [article]

Noor B Al-Sharif, Etienne St-Onge, Guillaume Theaud, Alan C Evans, Maxime Descoteaux
2020 bioRxiv   pre-print
Using structural processing techniques and related methods, a growing body of literature has illustrated that connectomics is a crucial aspect to assessing the brain in health and disease.  ...  The Pediatric Imaging Neurocognition and Genetics (PING) dataset was collected and released openly to contribute to the assessment of typical brain development in a pediatric sample.  ...  ., Connelly, A., 2019. Mrtrix3: A 560 fast, flexible and open software framework for medical image processing and visualisation. NeuroImage , 116137.  ... 
doi:10.1101/2020.11.24.396549 fatcat:juzb47l4vffu5jab2i3uadywse

Detecting Corticospinal Tract Impairment in Tumor Patients With Fiber Density and Tensor-Based Metrics

Lucius S. Fekonja, Ziqian Wang, Dogu B. Aydogan, Timo Roine, Melina Engelhardt, Felix R. Dreyer, Peter Vajkoczy, Thomas Picht
2021 Frontiers in Oncology  
Peritumoral values were lower for FA and FD, but higher for ADC within the entire cohort.  ...  The delineation of the healthy-pathological white matter (WM) interface area, for which diffusion magnetic resonance imaging (dMRI) has shown promising potential, may improve treatment outcome.  ...  MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation.  ... 
doi:10.3389/fonc.2020.622358 pmid:33585250 pmcid:PMC7873606 fatcat:gdradh3wkzbfdbfvwctbyzirsq

Brain microstructure and morphology of very preterm-born infants at term equivalent age: associations with motor and cognitive outcomes at 1 and 2 years

Kerstin Pannek, Joanne M. George, Roslyn N. Boyd, Paul B. Colditz, Stephen E. Rose, Jurgen Fripp
2020 NeuroImage  
Diffusion MRI data were processed using constrained spherical deconvolution (CSD) and aligned to a study-specific fibre orientation distribution template, yielding measures of fibre density (FD), fibre-bundle  ...  Brain magnetic resonance imaging (MRI) at term equivalent age (TEA) can probe tissue microstructure and morphology, and demonstrates potential in the early prediction of outcomes.  ...  Alan Connelly. 2019. 26 "MRtrix3: A Fast, Flexible and Open Software Framework for Medical Image Processing 27 and Visualisation."  ... 
doi:10.1016/j.neuroimage.2020.117163 pmid:32663645 fatcat:wco2lcwnjre7fmb4l6qwssoqra

Long-term development of white matter fibre density and morphology up to 13 years after preterm birth [article]

Claire E Kelly, Deanne K Thompson, Sila Genc, Jian Chen, Joseph YM Yang, Chris Adamson, Richard Beare, Marc L Seal, Lex W Doyle, Jeanie LY Cheong, Peter J Anderson
2020 medRxiv   pre-print
Methods: Diffusion images were acquired for a cohort of VP (born <30 weeks' gestation) and full-term (FT, ≥37 weeks' gestation) children at two ages: mean (SD) 7.6 (0.2) years (n=138 VP and 32 FT children  ...  ) and 13.3 (0.4) years (n=130 VP and 45 FT children). 103 VP and 21 FT children had images at both ages for longitudinal analysis.  ...  We thank members of the VIBeS and Developmental Imaging teams, the Royal Children's Hospital Medical Imaging staff for their assistance and expertise in the collection of the MRI data included in this  ... 
doi:10.1101/2020.04.01.20049585 fatcat:g5gqs6ou7nhqbaicy2a6plwzfq

Progression of Visual Pathway Degeneration in Primary Open-Angle Glaucoma: A Longitudinal Study

Shereif Haykal, Nomdo M. Jansonius, Frans W. Cornelissen
2021 Frontiers in Human Neuroscience  
This suggests the presence of a time window for salvaging intact post-geniculate pathways, which could prove to be a viable therapeutic target in the future.  ...  Furthermore, we find evidence that the trans-synaptic spread of glaucomatous degeneration to the post-geniculate pathways is a prolonged process which continues in the absence of detectable pre-geniculate  ...  MRtrix3: a fast, flexible and open software framework 26, 173–181. doi: 10.1097/IJG.0000000000000558 for medical image processing and visualisation.  ... 
doi:10.3389/fnhum.2021.630898 pmid:33854423 pmcid:PMC8039117 fatcat:t2akqzqsxzbcvhoevaj3qadomu

PPA: Principal Parcellation Analysis for Brain Connectomes and Multiple Traits [article]

Rongjie Liu, Meng Li, David B. Dunson
2022 arXiv   pre-print
Our PPA package is publicly available on GitHub, and can be implemented routinely for diffusion image data.  ...  In this article, we propose a novel tractography-based representation of brain connectomes, which clusters fiber endpoints to define a data adaptive parcellation targeted to explain variation among individuals  ...  Acknowledgements We thank Lu Wang for helpful discussions on implementing the SBL method, and Yerong  ... 
arXiv:2103.03478v2 fatcat:l3g5yn3y7jaozcvaelnkjbe6eq

Assessing the Reliability of Template-Based Clustering for Tractography in Healthy Human Adults

Jason Kai, Ali R. Khan
2022 Frontiers in Neuroinformatics  
A commonly used approach for identifying tracts is with template-based clustering, where unsupervised clustering is first performed on a template in order to label corresponding tracts in unseen data.  ...  The two different template-based approaches exhibited similar reliability for identifying both deep white matter tracts and the superficial white matter.  ...  MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation.  ... 
doi:10.3389/fninf.2022.777853 pmid:35250526 pmcid:PMC8891507 fatcat:hnow4nabwnagjkisqk3njqzoay

Microstructural Tissue Changes in a Rat Model of Mild Traumatic Brain Injury

Karthik Chary, Omar Narvaez, Raimo A. Salo, Isabel San Martín Molina, Jussi Tohka, Manisha Aggarwal, Olli Gröhn, Alejandra Sierra
2021 Frontiers in Neuroscience  
The brains of sham-operated and mTBI rats 35 days after lateral fluid percussion injury were imaged ex vivo in a 11.7-T scanner.  ...  Our study investigates the potential of diffusion MRI (dMRI), including diffusion tensor imaging (DTI), fixel-based analysis (FBA) and neurite orientation dispersion and density imaging (NODDI), to detect  ...  MRtrix3: a fast, flexible and open software framework for medical image processing and visualisation.  ... 
doi:10.3389/fnins.2021.746214 pmid:34899158 pmcid:PMC8662623 fatcat:yixkh4eebfdhnc7bu5eiwlc3vi

Dynamic Functional Connectivity Better Predicts Disability Than Structural and Static Functional Connectivity in People With Multiple Sclerosis

Ceren Tozlu, Keith Jamison, Susan A. Gauthier, Amy Kuceyeski
2021 Frontiers in Neuroscience  
Advanced imaging techniques such as diffusion and functional MRI can be used to identify pathology-related changes to the brain's structural and functional connectivity (SC and FC) networks and mapping  ...  On the other hand, dynamic FC metrics were most important for determining disability level in pwMS, and could represent functional compensation in response to white matter pathology in pwMS.  ...  MRtrix3: a fast, flexible and open software framework for medical image processing and visualisation.  ... 
doi:10.3389/fnins.2021.763966 pmid:34966255 pmcid:PMC8710545 fatcat:cav7e377abckjag7lu273jihdq

DNA methylation and brain dysmaturation in preterm infants [article]

Emily N W Wheater, Paola Galdi, Daniel McCartney, Manuel Blesa, Gemma Sullivan, David Q Stoye, Gillian Lamb, Sarah Sparrow, Lee Murphy, Nicola Wrobel, Alan J Quigley, Scott Semple (+6 others)
2021 medRxiv   pre-print
Finally, associations between differential DNAm and image markers of white matter tract microstructure suggest that variation in DNAm may provide a link between preterm birth and the dysconnectivity of  ...  Gestational age at birth has a profound and widely distributed effect on the neonatal saliva methylome.  ...  imaging research staff for providing the infant scanning.  ... 
doi:10.1101/2021.04.08.21255064 fatcat:3md7jk66fzfa3gocpbq3k2eqae
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