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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  
From a user's perspective, the hMRI-toolbox is an efficient, robust and simple framework for investigating qMRI data in neuroscience and clinical research.  ...  Thus, the current version of the toolbox is a first step towards in vivo histology using MRI (hMRI) and is being extended further in this direction.  ...  As such, the hMRI-toolbox is a comprehensive and readily extendable tool for estimating and processing qMRI data for neuroscience and clinical research.  ... 
doi:10.1016/j.neuroimage.2019.01.029 pmid:30677501 pmcid:PMC6547054 fatcat:6m7s4t2vajhshgybudevhuh3bi

hMRI - A toolbox for using quantitative MRI in neuroscience and clinical research [article]

Evelyne Balteau, Karsten Tabelow, John Ashburner, Martina F. Callaghan, Bogdan Draganski, Gunther Helms, Ferath Kherif, Tobias Leutritz, Antoine Lutti, Christophe Phillips, Enrico Reimer, Lars Ruthotto (+6 others)
The hMRI-toolbox is an efficient, robust and simple framework for investigating qMRI data in neuroscience and clinical research.  ...  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  ...  INTRODUCTION Quantitative MRI (qMRI) finds increasing interest in neuroscience and clinical research due to its greater specificity and its sensitivity to micro-structural properties of brain tissue such  ... 
doi:10.34657/2481 fatcat:x42eo46qmbbglot3cduerpxg7u

Example Dataset for the hMRI Toolbox

Martina F. Callaghan, Antoine Lutti, John Ashburner, Evelyne Balteau, Nadège Corbin, Bogdan Draganski, Gunther Helms, Ferath Kherif, Tobias Leutritz, Siawoosh Mohammadi, Christophe Phillips, Enrico Reimer (+5 others)
2019 Data in Brief  
can be found at, and following the theory described in: hMRI - A toolbox for quantitative MRI in neuroscience and clinical research [1].  ...  The hMRI toolbox is an open-source toolbox for the calculation of quantitative MRI parameter maps from a series of weighted imaging data, and optionally additional calibration data.  ...  personal relationships that could have appeared to influence the work reported in this paper.  ... 
doi:10.1016/j.dib.2019.104132 pmid:31297422 pmcid:PMC6598837 fatcat:v4eughbbq5hxzbqcd554izmjtq

qMRLab: Quantitative MRI analysis, under one umbrella

Agah Karakuzu, Mathieu Boudreau, Tanguy Duval, Tommy Boshkovski, Ilana Leppert, Jean-François Cabana, Ian Gagnon, Pascale Beliveau, G. Pike, Julien Cohen-Adad, Nikola Stikov
2020 Journal of Open Source Software  
The work is also funded in part by the Montreal Heart Institute Foundation, Canadian Open Neuroscience Platform (  ...  Acknowledgements This research was undertaken thanks, in part, to funding from the Canada First Research Excellence Fund through the TransMedTech Institute.  ...  While the vision for quantitative MRI is to overcome site-dependent variations, this is still a challenge due to variability in the hardware and software used by MR vendors to produce quantitative MRI  ... 
doi:10.21105/joss.02343 fatcat:buwcqr4c6rgv3m7hwcka3mjwdi

Restoring statistical validity in group analyses of motion-corrupted MRI data [article]

Antoine Lutti, Nadège Corbin, John Ashburner, Gabriel Ziegler, Bogdan Draganski, Christophe Phillips, Ferath Kherif, Martina F Callaghan, Giulia Di Domenicantonio
2021 biorxiv/medrxiv   pre-print
However, the criterion for exclusion is difficult to determine objectively and exclusion can lead to a suboptimal compromise between image quality and sample size.  ...  This method is amenable to the analysis of a broad type of MRI data and can accommodate any measure of image quality.  ...  The MRI data was acquired on the MRI platform of the Clinical Neuroscience Department, Lausanne University Hospital.  ... 
doi:10.1101/2021.06.15.448467 fatcat:vt5gjldiyrfrtk6ktcqjwxj4ga

Reducing susceptibility distortion related image blurring in diffusion MRI EPI data [article]

Ian A Clark, Martina F Callaghan, Nikolaus Weiskopf, Eleanor A Maguire, Siawoosh Mohammadi
2021 bioRxiv   pre-print
Diffusion magnetic resonance imaging (MRI) is an increasingly popular technique in basic and clinical neuroscience.  ...  as part of SPM, which can be easily combined with other SPM toolboxes, such as the hMRI toolbox, to facilitate computation of myelin biomarkers that are necessary for g-ratio mapping.  ...  ACKNOWLEDGEMENTS Thanks to Anna Monk, Victoria Hotchin and Gloria Pizzamiglio for assistance with data collection. Thanks also to Lars Rutthotto for helpful discussions.  ... 
doi:10.1101/2021.06.07.447406 fatcat:wgdm3q2txjcnhccyrx4xyespee

Quantitative Multi-Parameter Mapping Optimized for the Clinical Routine

Graham Cooper, Sebastian Hirsch, Michael Scheel, Alexander U. Brandt, Friedemann Paul, Carsten Finke, Philipp Boehm-Sturm, Stefan Hetzer
2020 Frontiers in Neuroscience  
Using quantitative multi-parameter mapping (MPM), studies can investigate clinically relevant microstructural changes with high reliability over time and across subjects and sites.  ...  Intra-subject variability for all four maps in white matter ranged from 1.2–5.3% and in gray matter from 1.8 to 9.2%.  ...  We would also like to thank Jakob Seja for his help in implementing the automated quantification pipeline in the clinical environment.  ... 
doi:10.3389/fnins.2020.611194 pmid:33364921 pmcid:PMC7750476 fatcat:w6wrv34dgrgabdo4n2zzenzrhm

Error quantification in multi-parameter mapping facilitates robust estimation and enhanced group level sensitivity [article]

Siawoosh Mohammadi, Tobias Streubel, Leonie Klock, Antoine Lutti, Kerrin Pine, Sandra Weber, Luke Edwards, Patrick Scheibe, Gabriel Ziegler, Jurgen Gallinat, Simone Kuhn, Martina Callaghan (+2 others)
2022 bioRxiv   pre-print
Code to compute the mSNR maps and robustly combined MPM maps is available in the open-source hMRI toolbox.  ...  Multi-Parameter Mapping (MPM) is a comprehensive quantitative neuroimaging protocol that enables estimation of four physical parameters (longitudinal and effective transverse relaxation rates R1 and R2  ...  Acknowledgements We would like to thank Saskia Helbling and Peter McColgan for sharing the 7T dataset originally published in (McColgan et al., 2021) .  ... 
doi:10.1101/2022.01.11.475846 fatcat:tcdiwyi7evdm3ihzy5d7jnktry

The Influence of Radio-Frequency Transmit Field Inhomogeneities on the Accuracy of G-ratio Weighted Imaging

Tim M. Emmenegger, Gergely David, Mohammad Ashtarayeh, Francisco J. Fritz, Isabel Ellerbrock, Gunther Helms, Evelyne Balteau, Patrick Freund, Siawoosh Mohammadi
2021 Frontiers in Neuroscience  
The data-driven correction is readily available in the open-source hMRI toolbox ( which is embedded in the statistical parameter mapping (SPM) framework.  ...  We found that it reduced the bias and error in the MR g-ratio by a factor of three.  ...  To differentiate such processes and understand their functional implications, neuroscience and clinical research would greatly benefit from in-vivo whole-brain measurements of MR g-ratio.  ... 
doi:10.3389/fnins.2021.674719 pmid:34290579 pmcid:PMC8287210 fatcat:m3wkmxzviffstfhpgdxzbpvokq

White matter tract myelin maturation and its association with general psychopathology in adolescence and early adulthood

Lucy D. Vanes, Michael Moutoussis, Gabriel Ziegler, Ian M. Goodyer, Peter Fonagy, Peter B. Jones, Edward T. Bullmore, Raymond J. Dolan, NSPN Consortium
2019 Human Brain Mapping  
Impaired myelin growth in limbic association fibres may serve as a neural marker for emerging mental illness during the course of adolescence and early adulthood.  ...  We then investigated its relationship to the expression of a general psychopathology "p-factor" in a longitudinal analysis of 293 healthy participants between the ages of 14 and 24.  ...  Semiquantitative MT saturation maps were derived using biophysical models as described in more detail in Helms, Dathe, Kallenberg, and Dechent (2008) and Tabelow et al. (2019) using the hMRI toolbox  ... 
doi:10.1002/hbm.24842 pmid:31661180 pmcid:PMC7268015 fatcat:bpo57n5vlvburd6ik4uuzskgqe

Apparent thinning of human visual cortex during childhood is associated with myelination

Vaidehi S. Natu, Jesse Gomez, Michael Barnett, Brianna Jeska, Evgeniya Kirilina, Carsten Jaeger, Zonglei Zhen, Siobhan Cox, Kevin S. Weiner, Nikolaus Weiskopf, Kalanit Grill-Spector
2019 Proceedings of the National Academy of Sciences of the United States of America  
Our data have broad ramifications for understanding both typical and atypical brain development using advanced in vivo quantitative measurements and clinical conditions implicating myelin.  ...  Using functional magnetic resonance imaging (fMRI), quantitative MRI (qMRI), and diffusion MRI (dMRI) in children and adults, we tested what quantitative changes occur to gray and white matter in ventral  ...  /hMRI-toolbox/) was used to reconstruct R 2 *, PD, and R 1 maps (84) .  ... 
doi:10.1073/pnas.1904931116 pmid:31548375 pmcid:PMC6789966 fatcat:ckkkwicosvdffef7xwzpl3owha

7 Tesla MRI Followed by Histological 3D Reconstructions in Whole-Brain Specimens

Anneke Alkemade, Kerrin Pine, Evgeniya Kirilina, Max C. Keuken, Martijn J. Mulder, Rawien Balesar, Josephine M. Groot, Ronald L. A. W. Bleys, Robert Trampel, Nikolaus Weiskopf, Andreas Herrler, Harald E. Möller (+2 others)
2020 Frontiers in Neuroanatomy  
For MRI, tissue was packed in a susceptibility matched solution, tailored to fit the dimensions of the MRI coil.  ...  Post mortem magnetic resonance imaging (MRI) studies on the human brain are of great interest for the validation of in vivo MRI.  ...  ACKNOWLEDGMENTS We are grateful to Toralf Mildner for his expert input on MRI scanning, and Domenica Wilfling and Suzanne Verlinde for excellent technical assistance.  ... 
doi:10.3389/fnana.2020.536838 pmid:33117133 pmcid:PMC7574789 fatcat:i7cjntg2mzhujjxa3ux7ji57zy

Childhood socio‐economic disadvantage predicts reduced myelin growth across adolescence and young adulthood

Gabriel Ziegler, Michael Moutoussis, Tobias U. Hauser, Pasco Fearon, Edward T. Bullmore, Ian M. Goodyer, Peter Fonagy, Peter B. Jones, Ulman Lindenberger, Raymond J. Dolan
2020 Human Brain Mapping  
This association was observed for magnetization transfer in cortical, subcortical and core white matter regions, and also in key subcortical nuclei.  ...  (MT), a myelin-sensitive marker, in 288 participants (149 female) between 14 and 25 years of age at baseline.  ...  /hMRI-group/Toolbox), Computational Anatomy toolbox (CAT12, http://www.neuro.uni-jena. de/cat/) and the tools described in more detail below and in Section 2 of the preceding paper that focussed on effects  ... 
doi:10.1002/hbm.25024 pmid:32432383 pmcid:PMC7375075 fatcat:x6vpq7t7fbgbhppwy44rsskcim

Hippocampal grey matter tissue microstructure does not explain individual differences in hippocampal-dependent task performance [article]

Ian A Clark, Martina F Callaghan, Nikolaus Weiskopf, Eleanor A Maguire
2020 bioRxiv   pre-print
for such relationships is, in fact, mixed.  ...  MRI data were collected using a multi-parameter mapping protocol from a large sample of 217 young, healthy adult participants with widely-varying task performance.  ...  J Neurosci 36:3552-3558 Tabelow K, Balteau E, Ashburner J et al. (2019) hMRI -A toolbox for quantitative MRI in neuroscience and clinical research.  ... 
doi:10.1101/2020.08.18.255992 fatcat:gpq6t7q4kjcddfnoawixdczuoq


2019 Clinical Neuroradiology  
Conclusion: We report about a rare case of bilateral temporomesial polymicrogyria in a 28-year old female patient as cause for structural epilepsy.  ...  A quantitative MRI water mapping sequence was conducted on a clinical 3 T system. Nonalcoholic fluid in-and output were documented and accounted for.  ...  , clinical symptoms, and MRI findings.  ... 
doi:10.1007/s00062-019-00826-9 fatcat:c6tdsym7jjc5dcduvvz7nxhcj4
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