1
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Vinh To X, Kurniawan ND, Cumming P, Nasrallah FA. A cross-comparative analysis of in vivo versus ex vivo MRI indices in a mouse model of concussion. Brain Res 2023; 1820:148562. [PMID: 37673379 DOI: 10.1016/j.brainres.2023.148562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/01/2023] [Accepted: 08/31/2023] [Indexed: 09/08/2023]
Abstract
BACKGROUND We present a cross-sectional, case-matched, and pair-wise comparison of structural magnetic resonance imaging (MRI), diffusion tensor imaging (DTI), and neurite orientation dispersion and density imaging (NODDI) measures in vivo and ex vivo in a mouse model of concussion, thus aiming to establish the concordance of structural and diffusion imaging findings in living brain and after fixation. METHODS We allocated 28 male mice aged 3-4 months to sham injury and concussion (CON) groups. CON mice had received a single concussive impact on day 0 and underwent MRI at day 2 (n = 9) or 7 (n = 10) post-impact, and sham control mice likewise underwent imaging at day 2 (n = 5) or 7 (n = 4). Immediately after the final scanning, we collected the perfusion-fixed brains, which were stored for imaging ex vivo 6-12 months later. We then compared the structural imaging, DTI, and NODDI results between different methods. RESULTS In vivo to ex vivo structural and DTI/NODDI findings were in notably poor agreement regarding the effects of concussion on structural integrity of the brain. COMPARISON WITH EXISTING METHODS ex vivo imaging was frequently done to study the effects of diseases and treatments, but our results showed that ex vivo and in vivo imaging can detect completely opposite and contradictory results. This is also the first study that compares in vivo and ex vivo NODDI. CONCLUSION Our findings call for caution in extrapolating translational capabilities obtained ex vivo to physiological measurements in vivo. The divergent findings may reflect fixation artefacts and the contribution of the glymphatic system changes.
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Affiliation(s)
- Xuan Vinh To
- The Queensland Brain Institute, The University of Queensland, Australia
| | | | - Paul Cumming
- Department of Nuclear Medicine, Bern University Hospital, Bern, Switzerland; School of Psychology and Counselling, Queensland University of Technology, Brisbane, Australia
| | - Fatima A Nasrallah
- The Queensland Brain Institute, The University of Queensland, Australia; Centre for Advanced Imaging, The University of Queensland, Australia.
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2
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Orset T, Royo J, Santin MD, Pouget P, Thiebaut de Schotten M. A new open, high-resolution, multishell, diffusion-weighted imaging dataset of the living squirrel monkey. Sci Data 2023; 10:224. [PMID: 37081025 PMCID: PMC10119165 DOI: 10.1038/s41597-023-02126-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 03/31/2023] [Indexed: 04/22/2023] Open
Abstract
Although very well adapted to brain study, Magnetic Resonance Imaging (MRI) remains limited by the facilities and capabilities required to acquire data, especially for non-human primates. Addressing the data gaps resulting from these limitations requires making data more accessible and open. In contempt of the regular use of Saimiri sciureus in neuroscience research, in vivo diffusion has yet to be openly available for this species. Here we built and made openly available a unique new resource consisting of a high-resolution, multishell diffusion-weighted dataset in the anesthetized Saimiri sciureus. The data were acquired on 11 individuals with an 11.7 T MRI scanner (isotropic resolution of 400 µm3). This paper presents an overview of our dataset and illustrates some of its possible use through example analyses. To assess the quality of our data, we analyzed long-range connections (whole-brain tractography), microstructure (Neurite Orientation Dispersion and Density Imaging), and axon diameter in the corpus callosum (ActiveAx). Constituting an essential new resource for primate evolution studies, all data are openly available.
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Affiliation(s)
- Thomas Orset
- Brain Connectivity and Behaviour Laboratory, Sorbonne University, Paris, France.
- Sorbonne University, Inserm U1127, CNRS UMR7225, UM75, ICM, Movement Investigation and Therapeutics Team, Paris, France.
| | - Julie Royo
- Brain Connectivity and Behaviour Laboratory, Sorbonne University, Paris, France
- Sorbonne University, Inserm U1127, CNRS UMR7225, UM75, ICM, Movement Investigation and Therapeutics Team, Paris, France
| | | | - Pierre Pouget
- Brain Connectivity and Behaviour Laboratory, Sorbonne University, Paris, France
- Sorbonne University, Inserm U1127, CNRS UMR7225, UM75, ICM, Movement Investigation and Therapeutics Team, Paris, France
| | - Michel Thiebaut de Schotten
- Brain Connectivity and Behaviour Laboratory, Sorbonne University, Paris, France
- Groupe d'Imagerie Neurofonctionnelle, Institut des Maladies Neurodégénératives-UMR 5293, CNRS, CEA University of Bordeaux, Bordeaux, France
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3
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Yendiki A, Aggarwal M, Axer M, Howard AF, van Cappellen van Walsum AM, Haber SN. Post mortem mapping of connectional anatomy for the validation of diffusion MRI. Neuroimage 2022; 256:119146. [PMID: 35346838 PMCID: PMC9832921 DOI: 10.1016/j.neuroimage.2022.119146] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 03/02/2022] [Accepted: 03/23/2022] [Indexed: 01/13/2023] Open
Abstract
Diffusion MRI (dMRI) is a unique tool for the study of brain circuitry, as it allows us to image both the macroscopic trajectories and the microstructural properties of axon bundles in vivo. The Human Connectome Project ushered in an era of impressive advances in dMRI acquisition and analysis. As a result of these efforts, the quality of dMRI data that could be acquired in vivo improved substantially, and large collections of such data became widely available. Despite this progress, the main limitation of dMRI remains: it does not image axons directly, but only provides indirect measurements based on the diffusion of water molecules. Thus, it must be validated by methods that allow direct visualization of axons but that can only be performed in post mortem brain tissue. In this review, we discuss methods for validating the various features of connectional anatomy that are extracted from dMRI, both at the macro-scale (trajectories of axon bundles), and at micro-scale (axonal orientations and other microstructural properties). We present a range of validation tools, including anatomic tracer studies, Klingler's dissection, myelin stains, label-free optical imaging techniques, and others. We provide an overview of the basic principles of each technique, its limitations, and what it has taught us so far about the accuracy of different dMRI acquisition and analysis approaches.
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Affiliation(s)
- Anastasia Yendiki
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, United States,Corresponding author (A. Yendiki)
| | - Manisha Aggarwal
- Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Markus Axer
- Forschungszentrum Jülich, Institute of Neuroscience and Medicine, Jülich, Germany,Department of Physics, University of Wuppertal Germany
| | - Amy F.D. Howard
- Wellcome Centre for Integrative Neuroimaging, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Anne-Marie van Cappellen van Walsum
- Department of Medical Imaging, Anatomy, Radboud University Medical Center, Nijmegen, the Netherland,Cognition and Behaviour, Donders Institute for Brain, Nijmegen, the Netherland
| | - Suzanne N. Haber
- Department of Pharmacology and Physiology, University of Rochester, Rochester, NY, United States,McLean Hospital, Belmont, MA, United States
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4
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Grier MD, Yacoub E, Adriany G, Lagore RL, Harel N, Zhang RY, Lenglet C, Uğurbil K, Zimmermann J, Heilbronner SR. Ultra-high field (10.5T) diffusion-weighted MRI of the macaque brain. Neuroimage 2022; 255:119200. [PMID: 35427769 PMCID: PMC9446284 DOI: 10.1016/j.neuroimage.2022.119200] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/08/2022] [Accepted: 04/07/2022] [Indexed: 11/26/2022] Open
Abstract
Diffu0sion-weighted magnetic resonance imaging (dMRI) is a non-invasive imaging technique that provides information about the barriers to the diffusion of water molecules in tissue. In the brain, this information can be used in several important ways, including to examine tissue abnormalities associated with brain disorders and to infer anatomical connectivity and the organization of white matter bundles through the use of tractography algorithms. However, dMRI also presents certain challenges. For example, historically, the biological validation of tractography models has shown only moderate correlations with anatomical connectivity as determined through invasive tract-tracing studies. Some of the factors contributing to such issues are low spatial resolution, low signal-to-noise ratios, and long scan times required for high-quality data, along with modeling challenges like complex fiber crossing patterns. Leveraging the capabilities provided by an ultra-high field scanner combined with denoising, we have acquired whole-brain, 0.58 mm isotropic resolution dMRI with a 2D-single shot echo planar imaging sequence on a 10.5 Tesla scanner in anesthetized macaques. These data produced high-quality tractograms and maps of scalar diffusion metrics in white matter. This work demonstrates the feasibility and motivation for in-vivo dMRI studies seeking to benefit from ultra-high fields.
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Affiliation(s)
- Mark D Grier
- Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455, United States
| | - Essa Yacoub
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN 55455, United States; Center for Neuroengineering, University of Minnesota, Minneapolis, MN 55455, United States
| | - Gregor Adriany
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN 55455, United States; Center for Neuroengineering, University of Minnesota, Minneapolis, MN 55455, United States
| | - Russell L Lagore
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN 55455, United States
| | - Noam Harel
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN 55455, United States; Department of Neurosurgery, University of Minnesota, Minneapolis, MN 55455, United States
| | - Ru-Yuan Zhang
- Institute of Psychology and Behavioral Science, Shanghai Jiao Tong University, Shanghai 200030, P.R. China; Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, P.R. China; Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN 55455, United States
| | - Christophe Lenglet
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN 55455, United States
| | - Kâmil Uğurbil
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN 55455, United States; Center for Neuroengineering, University of Minnesota, Minneapolis, MN 55455, United States
| | - Jan Zimmermann
- Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455, United States; Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN 55455, United States; Center for Neuroengineering, University of Minnesota, Minneapolis, MN 55455, United States; Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, United States
| | - Sarah R Heilbronner
- Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455, United States; Center for Neuroengineering, University of Minnesota, Minneapolis, MN 55455, United States.
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5
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Miller JV, Andre Q, Timmers I, Simons L, Rasic N, Lebel C, Noel M. Subclinical post-traumatic stress symptomology and brain structure in youth with chronic headaches. NEUROIMAGE-CLINICAL 2021; 30:102627. [PMID: 33812302 PMCID: PMC8053811 DOI: 10.1016/j.nicl.2021.102627] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 03/01/2021] [Accepted: 03/05/2021] [Indexed: 01/17/2023]
Abstract
ACEs and PTSS did not significantly differ between patients and healthy controls. Patients demonstrated greater corticolimbic connectivity compared to controls. Greater PTSS and less corticolimbic connectivity increased headache frequency. Less corticolimbic connectivity may indicate greater disease progression. Patients may be more vulnerable to the effects of PTSS compared to controls.
Background/aims Post-traumatic stress symptoms (PTSS) and chronic pain often co-occur at high rates in youth. PTSS may alter brain structure thereby contributing to headache chronicity. This study examined whether PTSS and altered limbic circuitry were associated with headache frequency in youth. Methods Thirty youth aged 10–18 years with chronic headaches and 30 age- and sex-matched controls underwent a 3T MRI scan. Volumes of the hippocampus and amygdala were obtained from T1-weighted images. Mean fractional anisotropy (FA, an index of white matter structure) axial and radial diffusivity values of the cingulum and uncinate fasciculus were extracted from diffusion-weighted images. Youth reported on their headaches daily, for one-month, and self-reported pubertal status, emotion regulation, adverse childhood experiences (ACEs) and PTSS using validated measures. Volumes of the hippocampus and amygdala and diffusivity values of the cingulum and uncinate were compared between patients and controls. Hierarchical linear regressions were used to examine the association between PTSS, subcortical volumes and/or diffusivity values and headache frequency. Results Mean FA values of the cingulum were higher in patients compared to controls (P = 0.02, Cohen’s d = 0.69). Greater PTSS (P = 0.04), smaller amygdala volumes (P = 0.01) and lower FA of the cingulum (P = 0.04) were associated with greater headache frequency, after accounting for age, puberty, pain duration, emotion regulation, and ACEs (Adjusted R2 ≥ 0.15). Headache frequency was associated with increases in radial diffusivity (P = 0.002, Adjusted R2 = 0.59), as opposed to axial diffusivity (n.s.). Conclusions PTSS, smaller amygdalar volume, and poorer cingulum structural connectivity were associated with headache frequency in youth, and may underlie headache chronicity.
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Affiliation(s)
- Jillian Vinall Miller
- Anesthesiology, Perioperative & Pain Medicine, University of Calgary, Calgary, AB, Canada; Vi Riddell Children's Pain & Rehabilitation Centre, Alberta Children's Hospital, Calgary, AB, Canada; Behaviour & The Developing Brain, Alberta Children's Hospital Research Institute, Calgary, AB, Canada.
| | - Quinn Andre
- Medicine, University of Alberta, Edmonton, AB, Canada
| | - Inge Timmers
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA, United States
| | - Laura Simons
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA, United States
| | - Nivez Rasic
- Anesthesiology, Perioperative & Pain Medicine, University of Calgary, Calgary, AB, Canada; Vi Riddell Children's Pain & Rehabilitation Centre, Alberta Children's Hospital, Calgary, AB, Canada; Behaviour & The Developing Brain, Alberta Children's Hospital Research Institute, Calgary, AB, Canada
| | - Catherine Lebel
- Behaviour & The Developing Brain, Alberta Children's Hospital Research Institute, Calgary, AB, Canada; Radiology, University of Calgary, Calgary, AB, Canada
| | - Melanie Noel
- Vi Riddell Children's Pain & Rehabilitation Centre, Alberta Children's Hospital, Calgary, AB, Canada; Behaviour & The Developing Brain, Alberta Children's Hospital Research Institute, Calgary, AB, Canada; Psychology, University of Calgary, Calgary, AB, Canada
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6
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Olesen JL, Østergaard L, Shemesh N, Jespersen SN. Beyond the diffusion standard model in fixed rat spinal cord with combined linear and planar encoding. Neuroimage 2021; 231:117849. [PMID: 33582270 DOI: 10.1016/j.neuroimage.2021.117849] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 01/20/2021] [Accepted: 02/04/2021] [Indexed: 10/22/2022] Open
Abstract
Information about tissue on the microscopic and mesoscopic scales can be accessed by modelling diffusion MRI signals, with the aim of extracting microstructure-specific biomarkers. The standard model (SM) of diffusion, currently the most broadly adopted microstructural model, describes diffusion in white matter (WM) tissues by two Gaussian components, one of which has zero radial diffusivity, to represent diffusion in intra- and extra-axonal water, respectively. Here, we reappraise these SM assumptions by collecting comprehensive double diffusion encoded (DDE) MRI data with both linear and planar encodings, which was recently shown to substantially enhance the ability to estimate SM parameters. We find however, that the SM is unable to account for data recorded in fixed rat spinal cord at an ultrahigh field of 16.4 T, suggesting that its underlying assumptions are violated in our experimental data. We offer three model extensions to mitigate this problem: first, we generalize the SM to accommodate finite radii (axons) by releasing the constraint of zero radial diffusivity in the intra-axonal compartment. Second, we include intracompartmental kurtosis to account for non-Gaussian behaviour. Third, we introduce an additional (third) compartment. The ability of these models to account for our experimental data are compared based on parameter feasibility and Bayesian information criterion. Our analysis identifies the three-compartment description as the optimal model. The third compartment exhibits slow diffusion with a minor but non-negligible signal fraction (∼12%). We demonstrate how failure to take the presence of such a compartment into account severely misguides inferences about WM microstructure. Our findings bear significance for microstructural modelling at large and can impact the interpretation of biomarkers extracted from the standard model of diffusion.
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Affiliation(s)
- Jonas L Olesen
- Center of Functionally Integrative Neuroscience (CFIN) and MINDLab, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark; Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark
| | - Leif Østergaard
- Center of Functionally Integrative Neuroscience (CFIN) and MINDLab, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Noam Shemesh
- Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Sune N Jespersen
- Center of Functionally Integrative Neuroscience (CFIN) and MINDLab, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark; Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark.
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7
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Zhou Z, Tong Q, Zhang L, Ding Q, Lu H, Jonkman LE, Yao J, He H, Zhu K, Zhong J. Evaluation of the diffusion MRI white matter tract integrity model using myelin histology and Monte-Carlo simulations. Neuroimage 2020; 223:117313. [PMID: 32882384 DOI: 10.1016/j.neuroimage.2020.117313] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 08/21/2020] [Accepted: 08/24/2020] [Indexed: 12/13/2022] Open
Abstract
Quantitative evaluation of brain myelination has drawn considerable attention. Conventional diffusion-based magnetic resonance imaging models, including diffusion tensor imaging and diffusion kurtosis imaging (DKI),1 have been used to infer the microstructure and its changes in neurological diseases. White matter tract integrity (WMTI) was proposed as a biophysical model to relate the DKI-derived metrics to the underlying microstructure. Although the model has been validated on ex vivo animal brains, it was not well evaluated with ex vivo human brains. In this study, histological samples (namely corpus callosum) from postmortem human brains have been investigated based on WMTI analyses on a clinical 3T scanner and comparisons with gold standard myelin staining in proteolipid protein and Luxol fast blue. In addition, Monte Carlo simulations were conducted to link changes from ex vivo to in vivo conditions based on the microscale parameters of water diffusivity and permeability. The results show that WMTI metrics, including axonal water fraction AWF, radial extra-axonal diffusivity De⊥, and intra-axonal diffusivity Dawere needed to characterize myelin content alterations. Thus, WMTI model metrics are shown to be promising candidates as sensitive biomarkers of demyelination.
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Affiliation(s)
- Zihan Zhou
- Center for Brain Imaging Science and Technology, Key Laboratory for Biomedical Engineering of Ministry of Education, College of Biomedical Engineering and Instrumental Science, Zhejiang University, Zhouyiqing Building, Room 314, Yuquan Campus, Hangzhou 310027, China
| | - Qiqi Tong
- Center for Brain Imaging Science and Technology, Key Laboratory for Biomedical Engineering of Ministry of Education, College of Biomedical Engineering and Instrumental Science, Zhejiang University, Zhouyiqing Building, Room 314, Yuquan Campus, Hangzhou 310027, China
| | - Lei Zhang
- China Brain Bank and Department of Neurology in Second Affiliated Hospital, Key Laboratory of Medical Neurobiology of Zhejiang Province, and Department of Neurobiology, Zhejiang University School of Medicine, Hangzhou 310058, China; Department of Pathology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Qiuping Ding
- Center for Brain Imaging Science and Technology, Key Laboratory for Biomedical Engineering of Ministry of Education, College of Biomedical Engineering and Instrumental Science, Zhejiang University, Zhouyiqing Building, Room 314, Yuquan Campus, Hangzhou 310027, China
| | - Hui Lu
- China Brain Bank and Department of Neurology in Second Affiliated Hospital, Key Laboratory of Medical Neurobiology of Zhejiang Province, and Department of Neurobiology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Laura E Jonkman
- Department of Anatomy and Neurosciences, Amsterdam Neuroscience, Amsterdam UMC, location VUmc, the Netherlands
| | - Junye Yao
- Center for Brain Imaging Science and Technology, Key Laboratory for Biomedical Engineering of Ministry of Education, College of Biomedical Engineering and Instrumental Science, Zhejiang University, Zhouyiqing Building, Room 314, Yuquan Campus, Hangzhou 310027, China
| | - Hongjian He
- Center for Brain Imaging Science and Technology, Key Laboratory for Biomedical Engineering of Ministry of Education, College of Biomedical Engineering and Instrumental Science, Zhejiang University, Zhouyiqing Building, Room 314, Yuquan Campus, Hangzhou 310027, China.
| | - Keqing Zhu
- China Brain Bank and Department of Neurology in Second Affiliated Hospital, Key Laboratory of Medical Neurobiology of Zhejiang Province, and Department of Neurobiology, Zhejiang University School of Medicine, Hangzhou 310058, China; Department of Pathology, Zhejiang University School of Medicine, Hangzhou 310058, China.
| | - Jianhui Zhong
- Center for Brain Imaging Science and Technology, Key Laboratory for Biomedical Engineering of Ministry of Education, College of Biomedical Engineering and Instrumental Science, Zhejiang University, Zhouyiqing Building, Room 314, Yuquan Campus, Hangzhou 310027, China; Department of Imaging Sciences, University of Rochester, United States
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8
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Boon BDC, Pouwels PJW, Jonkman LE, Keijzer MJ, Preziosa P, van de Berg WDJ, Geurts JJG, Scheltens P, Barkhof F, Rozemuller AJM, Bouwman FH, Steenwijk MD. Can post-mortem MRI be used as a proxy for in vivo? A case study. Brain Commun 2019; 1:fcz030. [PMID: 32954270 PMCID: PMC7425311 DOI: 10.1093/braincomms/fcz030] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 09/30/2019] [Accepted: 10/03/2019] [Indexed: 12/19/2022] Open
Abstract
Post-mortem in situ MRI has been used as an intermediate between brain histo(patho)logy and in vivo imaging. However, it is not known how comparable post-mortem in situ is to ante-mortem imaging. We report the unique situation of a patient with familial early-onset Alzheimer's disease due to a PSEN1 mutation, who underwent ante-mortem brain MRI and post-mortem in situ imaging only 4 days apart. T1-weighted and diffusion MRI was performed at 3-Tesla at both time points. Visual atrophy rating scales, brain volume, cortical thickness and diffusion measures were derived from both scans and compared. Post-mortem visual atrophy scores decreased 0.5-1 point compared with ante-mortem, indicating an increase in brain volume. This was confirmed by quantitative analysis; showing a 27% decrease of ventricular and 7% increase of whole-brain volume. This increase was more pronounced in the cerebellum and supratentorial white matter than in grey matter. Furthermore, axial and radial diffusivity decreased up to 60% post-mortem whereas average fractional anisotropy of white matter increased approximately 10%. This unique case study shows that the process of dying affects several imaging markers. These changes need to be taken into account when interpreting post-mortem MRI to make inferences on the in vivo situation.
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Affiliation(s)
- Baayla D C Boon
- Department of Neurology, Amsterdam Neuroscience, Alzheimer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HZ, Amsterdam, The Netherlands.,Department of Pathology, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HZ, Amsterdam, The Netherlands
| | - Petra J W Pouwels
- Department of Radiology and Nuclear Medicine, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HZ, Amsterdam, The Netherlands
| | - Laura E Jonkman
- Department of Anatomy and Neurosciences, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HZ, Amsterdam, The Netherlands
| | - Matthijs J Keijzer
- Department of Anatomy and Neurosciences, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HZ, Amsterdam, The Netherlands
| | - Paolo Preziosa
- Neuroimaging Research Unit, Division of Neuroscience, Institute of Experimental Neurology, San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Via Olgettina 60, 20132 Milan, Italy
| | - Wilma D J van de Berg
- Department of Anatomy and Neurosciences, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HZ, Amsterdam, The Netherlands
| | - Jeroen J G Geurts
- Department of Anatomy and Neurosciences, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HZ, Amsterdam, The Netherlands
| | - Philip Scheltens
- Department of Neurology, Amsterdam Neuroscience, Alzheimer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HZ, Amsterdam, The Netherlands
| | - Frederik Barkhof
- Department of Radiology and Nuclear Medicine, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HZ, Amsterdam, The Netherlands.,Institutes of Neurology and Healthcare Engineering, University College London, Gower Street, WC1E 6BT London, UK
| | - Annemieke J M Rozemuller
- Department of Pathology, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HZ, Amsterdam, The Netherlands
| | - Femke H Bouwman
- Department of Neurology, Amsterdam Neuroscience, Alzheimer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HZ, Amsterdam, The Netherlands
| | - Martijn D Steenwijk
- Department of Anatomy and Neurosciences, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HZ, Amsterdam, The Netherlands
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9
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Schilling KG, Gao Y, Stepniewska I, Janve V, Landman BA, Anderson AW. Histologically derived fiber response functions for diffusion MRI vary across white matter fibers-An ex vivo validation study in the squirrel monkey brain. NMR IN BIOMEDICINE 2019; 32:e4090. [PMID: 30908803 PMCID: PMC6525086 DOI: 10.1002/nbm.4090] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 01/25/2019] [Accepted: 02/16/2019] [Indexed: 06/09/2023]
Abstract
Understanding the relationship between the diffusion-weighted MRI signal and the arrangement of white matter fibers is fundamental for accurate voxel-wise reconstruction of the fiber orientation distribution (FOD) and subsequent fiber tractography. Spherical deconvolution reconstruction techniques model the diffusion signal as the convolution of the FOD with a response function that represents the signal profile of a single fiber orientation. Thus, given the signal and a fiber response function, the FOD can be estimated in every imaging voxel by deconvolution. However, the selection of the appropriate response function remains relatively under-studied, and requires further validation. In this work, using 3D histologically defined FODs and the corresponding diffusion signal from three ex vivo squirrel monkey brains, we derive the ground truth response functions. We find that the histologically derived response functions differ from those conventionally used. Next, we find that response functions statistically vary across brain regions, which suggests that the practice of using the same kernel throughout the brain is not optimal. We show that different kernels lead to different FOD reconstructions, which in turn can lead to different tractography results depending on algorithmic parameters, with large variations in the accuracy of resulting reconstructions. Together, these results suggest there is room for improvement in estimating and understanding the relationship between the diffusion signal and the underlying FOD.
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Affiliation(s)
- Kurt G Schilling
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Yurui Gao
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | | | - Vaibhav Janve
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Bennett A Landman
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
- Radiology and Radiological Sciences, Vanderbilt University, Nashville, TN, United States
- Department of Electrical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Adam W Anderson
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
- Radiology and Radiological Sciences, Vanderbilt University, Nashville, TN, United States
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10
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Rao JS, Liu Z, Zhao C, Wei RH, Liu RX, Zhao W, Zhou X, Tian PY, Yang ZY, Li XG. Image correction for diffusion tensor imaging of Rhesus monkey thoracic spinal cord. J Med Primatol 2019; 48:320-328. [PMID: 31148186 DOI: 10.1111/jmp.12422] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 04/03/2019] [Accepted: 05/12/2019] [Indexed: 02/02/2023]
Abstract
BACKGROUND The relatively tiny spinal cord of non-human primate (NHP) causes increased challenge in diffusion tensor imaging (DTI) post-processing. This study aimed to establish a reliable correction strategy applied to clinical DTI images of NHP. METHODS Six normal and partial spinal cord injury (SCI) rhesus monkeys underwent 3T MR scanning. A correction strategy combining multiple iterations and non-rigid deformation was used for DTI image post-processing. Quantitative evaluations were then conducted to investigate effects of distortion correction. RESULTS After correction, longitudinal geometric distortion, global distortion, and residual distance errors were all significantly decreased (P < 0.05). Fractional anisotropy at the injured site was remarkably lower than that at the contralateral site (P = 0.0488) and was substantially lower than those at the adjacent superior (P = 0.0157) and inferior (P = 0.0128) areas at the same side. CONCLUSIONS Our image correction strategy can improve the quality of the DTI images of NHP thoracic cords, contributing to the development of SCI preclinical research.
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Affiliation(s)
- Jia-Sheng Rao
- Beijing Key Laboratory for Biomaterials and Neural Regeneration, Department of Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China.,Beijing International Cooperation Bases for Science and Technology on Biomaterials and Neural Regeneration, Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing, China
| | - Zuxiang Liu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,Innovation Center of Excellence on Brain Science, Chinese Academy of Sciences, Beijing, China.,Department of Biology, College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Can Zhao
- Beijing International Cooperation Bases for Science and Technology on Biomaterials and Neural Regeneration, Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing, China.,Department of Measurement Control and Information Technology, School of Instrumentation and Optoelectronic Engineering, Beihang University, Beijing, China
| | - Rui-Han Wei
- Beijing Key Laboratory for Biomaterials and Neural Regeneration, Department of Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Ruo-Xi Liu
- Beijing Key Laboratory for Biomaterials and Neural Regeneration, Department of Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Wen Zhao
- Department of Neurobiology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Xia Zhou
- Beijing Key Laboratory for Biomaterials and Neural Regeneration, Department of Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Peng-Yu Tian
- Beijing Key Laboratory for Biomaterials and Neural Regeneration, Department of Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Zhao-Yang Yang
- Beijing International Cooperation Bases for Science and Technology on Biomaterials and Neural Regeneration, Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing, China.,Department of Neurobiology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Xiao-Guang Li
- Beijing Key Laboratory for Biomaterials and Neural Regeneration, Department of Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China.,Beijing International Cooperation Bases for Science and Technology on Biomaterials and Neural Regeneration, Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing, China
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11
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Nath V, Schilling KG, Remedios S, Bayrak RG, Gao Y, Blaber JA, Huo Y, Landman BA, Anderson AW. LEARNING 3D WHITE MATTER MICROSTRUCTURE FROM 2D HISTOLOGY. PROCEEDINGS. IEEE INTERNATIONAL SYMPOSIUM ON BIOMEDICAL IMAGING 2019; 2019:186-190. [PMID: 32211122 PMCID: PMC7092618 DOI: 10.1109/isbi.2019.8759388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Histological analysis is typically the gold standard for validating measures of tissue microstructure derived from magnetic resonance imaging (MRI) contrasts. However, most histological investigations are inherently 2-dimensional (2D), due to increased field-of-view, higher in-plane resolutions, ease of acquisition, decreased costs, and a large number of available contrasts compared to 3-dimensional (3D) analysis. Because of this, it would be of great interest to be able to learn the 3D tissue microstructure from 2D histology. In this study, we use diffusion MRI (dMRI) of a squirrel monkey brain and corresponding myelin stained sections in combination with a convolution neural network to learn the relationship between the 3D diffusion estimated axonal fiber orientation distributions and the 2D myelin stain. We find that we are able to estimate the 3D fiber distribution with moderate to high angular agreement with the ground truth (median angular correlation coefficients of 0.48 across the unseen slices). This network could be used to validate dMRI neuronal structural measurements in 3D, even if only 2D histology is available for validation. Generalization is possible to transfer this network to human stained sections to infer the 3D fiber distribution at resolutions currently unachievable with dMRI, which would allow diffusion fiber tractography at unprecedented resolutions. We envision the use of similar networks to learn other 3D microstructural measures from an array of potential common 2D histology contrasts.
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Affiliation(s)
- Vishwesh Nath
- Department of Computer Science, Vanderbilt University, Nashville, TN
| | - Kurt G Schilling
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN
| | - Samuel Remedios
- Department of Computer Science, Vanderbilt University, Nashville, TN
| | - Roza G Bayrak
- Department of Computer Science, Vanderbilt University, Nashville, TN
| | - Yurui Gao
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN
| | - Justin A Blaber
- Department of Electrical Engineering, Vanderbilt University, Nashville, TN
| | - Yuankai Huo
- Department of Computer Science, Vanderbilt University, Nashville, TN
| | - Bennett A Landman
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN
- Department of Computer Science, Vanderbilt University, Nashville, TN
- Department of Electrical Engineering, Vanderbilt University, Nashville, TN
| | - A W Anderson
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN
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12
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Schilling KG, Yeh FC, Nath V, Hansen C, Williams O, Resnick S, Anderson AW, Landman BA. A fiber coherence index for quality control of B-table orientation in diffusion MRI scans. Magn Reson Imaging 2019; 58:82-89. [PMID: 30682379 DOI: 10.1016/j.mri.2019.01.018] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 01/17/2019] [Accepted: 01/19/2019] [Indexed: 12/19/2022]
Abstract
PURPOSE The diffusion MRI "b-vector" table describing the diffusion sensitization direction can be flipped and permuted in dimension due to different orientation conventions used in scanners and incorrect or improperly utilized file formats. This can lead to incorrect fiber orientation estimates and subsequent tractography failure. Here, we present an automated quality control procedure to detect when the b-table is flipped and/or permuted incorrectly. METHODS We define a "fiber coherence index" to describe how well fibers are connected to each other, and use it to automatically detect the correct configuration of b-vectors. We examined the performance on 3981 research subject scans (Baltimore Longitudinal Study of Aging), 1065 normal subject scans of high image quality (Human Connectome Project), and 202 patient scans (Vanderbilt University Medical Center), as well as 9 in-vivo and 9 ex-vivo animal data. RESULTS The coherence index resulted in a 99.9% (3979/3981) and 100% (1065/1065) success rate in normal subject scans, 98% (198/202) in patient scans, and 100% (18/18) in both in-vivo and ex-vivo animal data in detecting the correct gradient table in datasets without severe image artifacts. The four failing cases (4/202) in patient scans, and two failures in healthy subject scans (2/3981), all showed prominent motion or signal dropout artifacts. CONCLUSIONS The fiber coherence measure can be used as an automatic quality assurance check in any diffusion analysis pipeline. Additionally, the success of this fiber coherence measure suggests potential broader applications, including evaluating data quality, or even providing diagnostic value as a biomarker of white matter integrity.
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Affiliation(s)
- Kurt G Schilling
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA.
| | - Fang-Cheng Yeh
- Department of Neurological Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, USA; Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Vishwesh Nath
- Electrical Engineering & Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Colin Hansen
- Department of Electrical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Owen Williams
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Susan Resnick
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Adam W Anderson
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA; Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Bennett A Landman
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA; Department of Electrical Engineering, Vanderbilt University, Nashville, TN, USA; Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
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13
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Sébille SB, Rolland AS, Welter ML, Bardinet E, Santin MD. Post mortem high resolution diffusion MRI for large specimen imaging at 11.7 T with 3D segmented echo-planar imaging. J Neurosci Methods 2019; 311:222-234. [PMID: 30321565 DOI: 10.1016/j.jneumeth.2018.10.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 10/09/2018] [Accepted: 10/10/2018] [Indexed: 11/25/2022]
Abstract
BACKGROUND Diffusion weighted imaging (DWI) is the only in vivo technique allowing for the mapping of tissue fiber architecture. Post mortem DWI is an increasingly popular method, since longer acquisition times (compared to in vivo) allow higher spatial and angular resolutions to be achieved. However, DWI protocols must be adapted to post mortem tissue (e.g., tuning acquisition parameters to account for changes in T1/T2). New method: In this work, we developed a framework to obtain high quality diffusion weighted images on post mortem large samples by using a combination of fast imaging with 3D diffusion-weighted segmented EPI (3D-DW seg-EPI), Gadolinium soaking and data denoising. Analyses including tractography were used to check the quality of the acquired data, including a comparison with 3D-DW SE acquisitions. Comparison with existing method: Effects on diffusion data of each of the components of the framework were tested: 3D-DW seg-EPI versus 3D-DW SE EPI; with and without data denoising; with and without Gd-soaking. CONCLUSIONS Our study demonstrated the feasibility of analysing anatomical connectivity using diffusion imaging of a post mortem macaque brain with a 3D-DW seg-EPI sequence acquired at ultra-high field. The combination of high angular and spatial resolution DWI with Gd-soaking and denoising provided data allowing us to perform diffusion tractography with results very similar to those obtained with a 3D-DW SE acquisition (with shorter acquisition times: 222 h versus 37 h for 3D-DW seg-EPI).
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Affiliation(s)
- Sophie Bernadette Sébille
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, INSERM, APHP GH Pitié-Salpêtrière, Institut du cerveau et de la moelle épinière (ICM), F-75013 Paris, France; Centre de Neuro-Imagerie de Recherche (CENIR), Paris, France
| | - Anne-Sophie Rolland
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, INSERM, APHP GH Pitié-Salpêtrière, Institut du cerveau et de la moelle épinière (ICM), F-75013 Paris, France
| | - Marie-Laure Welter
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, INSERM, APHP GH Pitié-Salpêtrière, Institut du cerveau et de la moelle épinière (ICM), F-75013 Paris, France
| | - Eric Bardinet
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, INSERM, APHP GH Pitié-Salpêtrière, Institut du cerveau et de la moelle épinière (ICM), F-75013 Paris, France; Centre de Neuro-Imagerie de Recherche (CENIR), Paris, France
| | - Mathieu David Santin
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, INSERM, APHP GH Pitié-Salpêtrière, Institut du cerveau et de la moelle épinière (ICM), F-75013 Paris, France; Centre de Neuro-Imagerie de Recherche (CENIR), Paris, France.
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14
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Schilling KG, Nath V, Hansen C, Parvathaneni P, Blaber J, Gao Y, Neher P, Aydogan DB, Shi Y, Ocampo-Pineda M, Schiavi S, Daducci A, Girard G, Barakovic M, Rafael-Patino J, Romascano D, Rensonnet G, Pizzolato M, Bates A, Fischi E, Thiran JP, Canales-Rodríguez EJ, Huang C, Zhu H, Zhong L, Cabeen R, Toga AW, Rheault F, Theaud G, Houde JC, Sidhu J, Chamberland M, Westin CF, Dyrby TB, Verma R, Rathi Y, Irfanoglu MO, Thomas C, Pierpaoli C, Descoteaux M, Anderson AW, Landman BA. Limits to anatomical accuracy of diffusion tractography using modern approaches. Neuroimage 2018; 185:1-11. [PMID: 30317017 DOI: 10.1016/j.neuroimage.2018.10.029] [Citation(s) in RCA: 144] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 09/14/2018] [Accepted: 10/09/2018] [Indexed: 12/12/2022] Open
Abstract
Diffusion MRI fiber tractography is widely used to probe the structural connectivity of the brain, with a range of applications in both clinical and basic neuroscience. Despite widespread use, tractography has well-known pitfalls that limits the anatomical accuracy of this technique. Numerous modern methods have been developed to address these shortcomings through advances in acquisition, modeling, and computation. To test whether these advances improve tractography accuracy, we organized the 3-D Validation of Tractography with Experimental MRI (3D-VoTEM) challenge at the ISBI 2018 conference. We made available three unique independent tractography validation datasets - a physical phantom and two ex vivo brain specimens - resulting in 176 distinct submissions from 9 research groups. By comparing results over a wide range of fiber complexities and algorithmic strategies, this challenge provides a more comprehensive assessment of tractography's inherent limitations than has been reported previously. The central results were consistent across all sub-challenges in that, despite advances in tractography methods, the anatomical accuracy of tractography has not dramatically improved in recent years. Taken together, our results independently confirm findings from decades of tractography validation studies, demonstrate inherent limitations in reconstructing white matter pathways using diffusion MRI data alone, and highlight the need for alternative or combinatorial strategies to accurately map the fiber pathways of the brain.
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Affiliation(s)
- Kurt G Schilling
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA.
| | - Vishwesh Nath
- Electrical Engineering & Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Colin Hansen
- Department of Electrical Engineering, Vanderbilt University, Nashville, TN, USA
| | | | - Justin Blaber
- Department of Electrical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Yurui Gao
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA
| | - Peter Neher
- Division of Medical Image Computing, German Cancer Research Center, Heidelberg, Germany
| | - Dogu Baran Aydogan
- Laboratory of Neuro Imaging (LONI), USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Yonggang Shi
- Laboratory of Neuro Imaging (LONI), USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Simona Schiavi
- Computer Science Department, University of Verona, Verona, Italy
| | | | - Gabriel Girard
- Signal Processing Lab (LTS5), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Muhamed Barakovic
- Signal Processing Lab (LTS5), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Jonathan Rafael-Patino
- Signal Processing Lab (LTS5), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - David Romascano
- Signal Processing Lab (LTS5), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Gaëtan Rensonnet
- Signal Processing Lab (LTS5), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Marco Pizzolato
- Signal Processing Lab (LTS5), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Alice Bates
- Signal Processing Lab (LTS5), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Elda Fischi
- Signal Processing Lab (LTS5), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Jean-Philippe Thiran
- Signal Processing Lab (LTS5), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Radiology Department, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland
| | - Erick J Canales-Rodríguez
- Signal Processing Lab (LTS5), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Radiology Department, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland
| | - Chao Huang
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hongtu Zhu
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Liming Zhong
- Guangdong Provincial Key Laboratory of Medical Image Processing, School of Biomedical Engineering, Southern Medical University, Guangzhou, China
| | - Ryan Cabeen
- Laboratory of Neuro Imaging (LONI), USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Arthur W Toga
- Laboratory of Neuro Imaging (LONI), USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Francois Rheault
- Sherbrooke Connectivity Imaging Lab (SCIL), Computer Science Department, Université de Sherbrooke, Canada
| | - Guillaume Theaud
- Sherbrooke Connectivity Imaging Lab (SCIL), Computer Science Department, Université de Sherbrooke, Canada
| | - Jean-Christophe Houde
- Sherbrooke Connectivity Imaging Lab (SCIL), Computer Science Department, Université de Sherbrooke, Canada
| | - Jasmeen Sidhu
- Sherbrooke Connectivity Imaging Lab (SCIL), Computer Science Department, Université de Sherbrooke, Canada
| | - Maxime Chamberland
- Cardiff University, Brain Research Imaging Centre, School of Psychology, Cardiff, UK
| | | | - Tim B Dyrby
- Danish Research Centre for Magnetic Resonance, Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark; Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ragini Verma
- Center for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia, PA, USA
| | - Yogesh Rathi
- Brigham and Women's Hospital, Harvard Medical School, USA
| | - M Okan Irfanoglu
- National Institute of Biomedical Imaging and Bioengineering, NIH, Bethesda, MD, USA
| | - Cibu Thomas
- Section on Learning and Plasticity, Laboratory of Brain and Cognition, NIMH, Bethesda, MD, USA
| | - Carlo Pierpaoli
- National Institute of Biomedical Imaging and Bioengineering, NIH, Bethesda, MD, USA
| | - Maxime Descoteaux
- Sherbrooke Connectivity Imaging Lab (SCIL), Computer Science Department, Université de Sherbrooke, Canada
| | - Adam W Anderson
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA; Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Bennett A Landman
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA; Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA; Department of Electrical Engineering, Vanderbilt University, Nashville, TN, USA
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15
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Schilling KG, Gao Y, Stepniewska I, Janve V, Landman BA, Anderson AW. Anatomical accuracy of standard-practice tractography algorithms in the motor system - A histological validation in the squirrel monkey brain. Magn Reson Imaging 2018; 55:7-25. [PMID: 30213755 DOI: 10.1016/j.mri.2018.09.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 08/06/2018] [Accepted: 09/06/2018] [Indexed: 01/15/2023]
Abstract
For two decades diffusion fiber tractography has been used to probe both the spatial extent of white matter pathways and the region to region connectivity of the brain. In both cases, anatomical accuracy of tractography is critical for sound scientific conclusions. Here we assess and validate the algorithms and tractography implementations that have been most widely used - often because of ease of use, algorithm simplicity, or availability offered in open source software. Comparing forty tractography results to a ground truth defined by histological tracers in the primary motor cortex on the same squirrel monkey brains, we assess tract fidelity on the scale of voxels as well as over larger spatial domains or regional connectivity. No algorithms are successful in all metrics, and, in fact, some implementations fail to reconstruct large portions of pathways or identify major points of connectivity. The accuracy is most dependent on reconstruction method and tracking algorithm, as well as the seed region and how this region is utilized. We also note a tremendous variability in the results, even though the same MR images act as inputs to all algorithms. In addition, anatomical accuracy is significantly decreased at increased distances from the seed. An analysis of the spatial errors in tractography reveals that many techniques have trouble properly leaving the gray matter, and many only reveal connectivity to adjacent regions of interest. These results show that the most commonly implemented algorithms have several shortcomings and limitations, and choices in implementations lead to very different results. This study should provide guidance for algorithm choices based on study requirements for sensitivity, specificity, or the need to identify particular connections, and should serve as a heuristic for future developments in tractography.
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Affiliation(s)
- Kurt G Schilling
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA; Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA.
| | - Yurui Gao
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA; Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | | | - Vaibhav Janve
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA; Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Bennett A Landman
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA; Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA; Radiology and Radiological Sciences, Vanderbilt University, Nashville, TN, USA; Department of Electrical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Adam W Anderson
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA; Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA; Radiology and Radiological Sciences, Vanderbilt University, Nashville, TN, USA
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16
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Tounekti S, Troalen T, Bihan-Poudec Y, Froesel M, Lamberton F, Ozenne V, Cléry J, Richard N, Descoteaux M, Ben Hamed S, Hiba B. High-resolution 3D diffusion tensor MRI of anesthetized rhesus macaque brain at 3T. Neuroimage 2018; 181:149-161. [PMID: 29960088 DOI: 10.1016/j.neuroimage.2018.06.045] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 06/11/2018] [Accepted: 06/13/2018] [Indexed: 12/16/2022] Open
Abstract
Diffusion Magnetic Resonance Imaging (dMRI) has been widely used to investigate human brain microstructure and connectivity and its abnormalities in a variety of brain deficits, whether acute, neurodevelopmental or neurodegenerative. However, the biological interpretation and validation of dMRI data modelling is still a crucial challenge in the field. In this respect, achieving high spatial resolution in-vivo dMRI in the non-human primate to compare these observations both with human dMRI on the one hand and 'ground truth' microstructural and histological data on the other hand is of outmost importance. Here, we developed a dMRI pulse sequence based on 3D-multishot Echo Planar Imaging (3D-msEPI) on a 3T human clinical scanner. We demonstrate the feasibility of cerebral dMRI at an isotropic resolution of 0.5 mm in 4 anesthetized macaque monkeys. The added value of the high-resolution dMRI is illustrated by focusing on two aspects. First, we show an enhanced descriptive power of the fine substructure of the hippocampus. Second, we show a more physiological description of the interface between cortex grey matter, superficial and deep white matter. Overall, the high spatial resolution dMRI acquisition method proposed in this study is a significant achievement with respect to the state of the art of dMRI on anesthetized monkeys. This study highlights also the potential of very high-resolution dMRI to precisely capture the microstructure of thin cerebral structures such as the hippocampus and superficial white matter.
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Affiliation(s)
- Slimane Tounekti
- Centre de Neuroscience Cognitive, CNRS UMR 5229, Université Claude Bernard Lyon I, France; Siemens Healthcare SAS, Saint-Denis, France
| | | | - Yann Bihan-Poudec
- Centre de Neuroscience Cognitive, CNRS UMR 5229, Université Claude Bernard Lyon I, France
| | - Mathilda Froesel
- Centre de Neuroscience Cognitive, CNRS UMR 5229, Université Claude Bernard Lyon I, France
| | | | - Valéry Ozenne
- Liryc -Centre de recherche cardio-thoracique U1045, Université de Bordeaux, France
| | - Justine Cléry
- Centre de Neuroscience Cognitive, CNRS UMR 5229, Université Claude Bernard Lyon I, France
| | - Nathalie Richard
- Centre de Neuroscience Cognitive, CNRS UMR 5229, Université Claude Bernard Lyon I, France
| | - Maxime Descoteaux
- Sherbrooke Connectivity Imaging Lab (SCIL), University of Sherbrooke, Sherbrooke, QC, Canada
| | - Suliann Ben Hamed
- Centre de Neuroscience Cognitive, CNRS UMR 5229, Université Claude Bernard Lyon I, France
| | - Bassem Hiba
- Centre de Neuroscience Cognitive, CNRS UMR 5229, Université Claude Bernard Lyon I, France.
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17
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Schilling KG, Gao Y, Stepniewska I, Wu TL, Wang F, Landman BA, Gore JC, Chen LM, Anderson AW. The VALiDATe29 MRI Based Multi-Channel Atlas of the Squirrel Monkey Brain. Neuroinformatics 2018; 15:321-331. [PMID: 28748393 DOI: 10.1007/s12021-017-9334-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
We describe the development of the first digital atlas of the normal squirrel monkey brain and present the resulting product, VALiDATe29. The VALiDATe29 atlas is based on multiple types of magnetic resonance imaging (MRI) contrast acquired on 29 squirrel monkeys, and is created using unbiased, nonlinear registration techniques, resulting in a population-averaged stereotaxic coordinate system. The atlas consists of multiple anatomical templates (proton density, T1, and T2* weighted), diffusion MRI templates (fractional anisotropy and mean diffusivity), and ex vivo templates (fractional anisotropy and a structural MRI). In addition, the templates are combined with histologically defined cortical labels, and diffusion tractography defined white matter labels. The combination of intensity templates and image segmentations make this atlas suitable for the fundamental atlas applications of spatial normalization and label propagation. Together, this atlas facilitates 3D anatomical localization and region of interest delineation, and enables comparisons of experimental data across different subjects or across different experimental conditions. This article describes the atlas creation and its contents, and demonstrates the use of the VALiDATe29 atlas in typical applications. The atlas is freely available to the scientific community.
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Affiliation(s)
- Kurt G Schilling
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA. .,Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA.
| | - Yurui Gao
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA.,Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | | | - Tung-Lin Wu
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA.,Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Feng Wang
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA.,Radiology and Radiological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Bennett A Landman
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA.,Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA.,Radiology and Radiological Sciences, Vanderbilt University, Nashville, TN, USA.,Department of Electrical Engineering, Vanderbilt University, Nashville, TN, USA
| | - John C Gore
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA.,Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA.,Radiology and Radiological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Li Min Chen
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA.,Radiology and Radiological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Adam W Anderson
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA.,Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA.,Radiology and Radiological Sciences, Vanderbilt University, Nashville, TN, USA
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18
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Nath V, Schilling KG, Parvathaneni P, Blaber J, Hainline AE, Ding Z, Anderson A, Landman BA. Empirical estimation of intravoxel structure with persistent angular structure and Q-ball models of diffusion weighted MRI. J Med Imaging (Bellingham) 2018; 5:014005. [PMID: 29531965 PMCID: PMC5838516 DOI: 10.1117/1.jmi.5.1.014005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 02/12/2018] [Indexed: 11/14/2022] Open
Abstract
The diffusion tensor model is nonspecific in regions where micrometer structural patterns are inconsistent at the millimeter scale (i.e., brain regions with pathways that cross, bend, branch, fan, etc.). Numerous models have been proposed to represent crossing fibers and complex intravoxel structure from in vivo diffusion weighted magnetic resonance imaging (e.g., high angular resolution diffusion imaging-HARDI). Here, we present an empirical comparison of two HARDI approaches-persistent angular structure MRI (PAS-MRI) and Q-ball-using a newly acquired reproducibility dataset. Briefly, a single subject was scanned 11 times with 96 diffusion weighted directions and 10 reference volumes for each of two [Formula: see text] values (1000 and [Formula: see text] for a total of 2144 volumes). Empirical reproducibility of intravoxel fiber fractions (number/strength of peaks), angular orientation, and fractional anisotropy was compared with metrics from a traditional tensor analysis approach, focusing on [Formula: see text] values of 1000 and [Formula: see text]. PAS-MRI is shown to be more reproducible than Q-ball and offers advantages at low [Formula: see text] values. However, there are substantial and biologically meaningful differences between the intravoxel structures estimated both in terms of analysis method as well as by [Formula: see text] value. The two methods suggest a fundamentally different microarchitecture of the human brain; therefore, it is premature to perform meta-analysis or combine results across HARDI studies using a different analysis model or acquisition sequences.
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Affiliation(s)
- Vishwesh Nath
- Vanderbilt University, Electrical Engineering and Computer Science, Nashville, Tennessee, United States
| | - Kurt G. Schilling
- Vanderbilt University, Vanderbilt University Institute of Imaging Science, Nashville, Tennessee, United States
| | - Prasanna Parvathaneni
- Vanderbilt University, Electrical Engineering and Computer Science, Nashville, Tennessee, United States
| | - Justin Blaber
- Vanderbilt University, Electrical Engineering and Computer Science, Nashville, Tennessee, United States
| | - Allison E. Hainline
- Vanderbilt University, Department of Biostatistics, Nashville, Tennessee, United States
| | - Zhaohua Ding
- Vanderbilt University, Vanderbilt University Institute of Imaging Science, Nashville, Tennessee, United States
| | - Adam Anderson
- Vanderbilt University, Vanderbilt University Institute of Imaging Science, Nashville, Tennessee, United States
| | - Bennett A. Landman
- Vanderbilt University, Electrical Engineering and Computer Science, Nashville, Tennessee, United States
- Vanderbilt University, Vanderbilt University Institute of Imaging Science, Nashville, Tennessee, United States
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19
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Schilling KG, Janve V, Gao Y, Stepniewska I, Landman BA, Anderson AW. Histological validation of diffusion MRI fiber orientation distributions and dispersion. Neuroimage 2017; 165:200-221. [PMID: 29074279 DOI: 10.1016/j.neuroimage.2017.10.046] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 10/04/2017] [Accepted: 10/21/2017] [Indexed: 12/13/2022] Open
Abstract
Diffusion magnetic resonance imaging (dMRI) is widely used to probe tissue microstructure, and is currently the only non-invasive way to measure the brain's fiber architecture. While a large number of approaches to recover the intra-voxel fiber structure have been utilized in the scientific community, a direct, 3D, quantitative validation of these methods against relevant histological fiber geometries is lacking. In this study, we investigate how well different high angular resolution diffusion imaging (HARDI) models and reconstruction methods predict the ground-truth histologically defined fiber orientation distribution (FOD), as well as investigate their behavior over a range of physical and experimental conditions. The dMRI methods tested include constrained spherical deconvolution (CSD), Q-ball imaging (QBI), diffusion orientation transform (DOT), persistent angular structure (PAS), and neurite orientation dispersion and density imaging (NODDI) methods. Evaluation criteria focus on overall agreement in FOD shape, correct assessment of the number of fiber populations, and angular accuracy in orientation. In addition, we make comparisons of the histological orientation dispersion with the fiber spread determined from the dMRI methods. As a general result, no HARDI method outperformed others in all quality criteria, with many showing tradeoffs in reconstruction accuracy. All reconstruction techniques describe the overall continuous angular structure of the histological FOD quite well, with good to moderate correlation (median angular correlation coefficient > 0.70) in both single- and multiple-fiber voxels. However, no method is consistently successful at extracting discrete measures of the number and orientations of FOD peaks. The major inaccuracies of all techniques tend to be in extracting local maxima of the FOD, resulting in either false positive or false negative peaks. Median angular errors are ∼10° for the primary fiber direction and ∼20° for the secondary fiber, if present. For most methods, these results did not vary strongly over a wide range of acquisition parameters (number of diffusion weighting directions and b value). Regardless of acquisition parameters, all methods show improved successes at resolving multiple fiber compartments in a voxel when fiber populations cross at near-orthogonal angles, with no method adequately capturing low to moderate angle (<60°) crossing fibers. Finally, most methods are limited in their ability to capture orientation dispersion, resulting in low to moderate, yet statistically significant, correlation with histologically-derived dispersion with both HARDI and NODDI methodologies. Together, these results provide quantitative measures of the reliability and limitations of dMRI reconstruction methods and can be used to identify relative advantages of competing approaches as well as potential strategies for improving accuracy.
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Affiliation(s)
- Kurt G Schilling
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA; Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA.
| | - Vaibhav Janve
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA; Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Yurui Gao
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA; Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | | | - Bennett A Landman
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA; Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA; Radiology and Radiological Sciences, Vanderbilt University, Nashville, TN, United States; Department of Electrical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Adam W Anderson
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA; Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA; Radiology and Radiological Sciences, Vanderbilt University, Nashville, TN, United States
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