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Hacker BJ, Imms PE, Dharani AM, Zhu J, Chowdhury NF, Chaudhari NN, Irimia A. Identification and Connectomic Profiling of Concussion Using Bayesian Machine Learning. J Neurotrauma 2024. [PMID: 38482793 DOI: 10.1089/neu.2023.0509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2024] Open
Abstract
Accurate early diagnosis of concussion is useful to prevent sequelae and improve neurocognitive outcomes. Early after head impact, concussion diagnosis may be doubtful in persons whose neurological, neuroradiological, and/or neurocognitive examinations are equivocal. Such individuals can benefit from novel accurate assessments that complement clinical diagnostics. We introduce a Bayesian machine learning classifier to identify concussion through cortico-cortical connectome mapping from magnetic resonance imaging in persons with quasi-normal cognition and without neuroradiological findings. Classifier features are generated from connectivity matrices specifying the mean fractional anisotropy of white matter connections linking brain structures. Each connection's saliency to classification was quantified by training individual classifier instantiations using a single feature type. The classifier was tested on a discovery sample of 92 healthy controls (HCs; 26 females, age μ ± σ: 39.8 ± 15.5 years) and 471 adult mTBI patients (158 females, age μ ± σ: 38.4 ± 5.9 years). Results were replicated in an independent validation sample of 256 HCs (149 females, age μ ± σ: 55.3 ± 12.1 years) and 126 patients with concussion (46 females, age μ ± σ: 39.0 ± 17.7 years). Classifier accuracy exceeds 99% in both samples, suggesting robust generalizability to new samples. Notably, 13 bilateral cortico-cortical connection pairs predict diagnostic status with accuracy exceeding 99% in both discovery and validation samples. Many such connection pairs are between prefrontal cortex structures, fronto-limbic and fronto-subcortical structures, and occipito-temporal structures in the ventral ("what") visual stream. This and related connectivity form a highly salient network of brain connections that is particularly vulnerable to concussion. Because these connections are important in mediating cognitive control, memory, and attention, our findings explain the high frequency of cognitive disturbances after concussion. Our classifier was trained and validated on concussed participants with cognitive profiles very similar to those of HCs. This suggests that the classifier can complement current diagnostics by providing independent information in clinical contexts where patients have quasi-normal cognition but where concussion diagnosis stands to benefit from additional evidence.
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Affiliation(s)
- Benjamin J Hacker
- Ethel Percy Andrus Gerontology Center, Leonard Davis School of Gerontology, Dana and David Dornsife College of Arts and Sciences, University of Southern California, Los Angeles, California, USA
- Mork Family Department of Chemical Engineering and Materials Science, Viterbi School of Engineering, Dana and David Dornsife College of Arts and Sciences, University of Southern California, Los Angeles, California, USA
| | - Phoebe E Imms
- Ethel Percy Andrus Gerontology Center, Leonard Davis School of Gerontology, Dana and David Dornsife College of Arts and Sciences, University of Southern California, Los Angeles, California, USA
| | - Ammar M Dharani
- Ethel Percy Andrus Gerontology Center, Leonard Davis School of Gerontology, Dana and David Dornsife College of Arts and Sciences, University of Southern California, Los Angeles, California, USA
| | - Jessica Zhu
- Corwin D. Denney Research Center, Alfred E. Mann Department of Biomedical Engineering, Viterbi School of Engineering, Dana and David Dornsife College of Arts and Sciences, University of Southern California, Los Angeles, California, USA
| | - Nahian F Chowdhury
- Ethel Percy Andrus Gerontology Center, Leonard Davis School of Gerontology, Dana and David Dornsife College of Arts and Sciences, University of Southern California, Los Angeles, California, USA
| | - Nikhil N Chaudhari
- Ethel Percy Andrus Gerontology Center, Leonard Davis School of Gerontology, Dana and David Dornsife College of Arts and Sciences, University of Southern California, Los Angeles, California, USA
- Corwin D. Denney Research Center, Alfred E. Mann Department of Biomedical Engineering, Viterbi School of Engineering, Dana and David Dornsife College of Arts and Sciences, University of Southern California, Los Angeles, California, USA
| | - Andrei Irimia
- Ethel Percy Andrus Gerontology Center, Leonard Davis School of Gerontology, Dana and David Dornsife College of Arts and Sciences, University of Southern California, Los Angeles, California, USA
- Corwin D. Denney Research Center, Alfred E. Mann Department of Biomedical Engineering, Viterbi School of Engineering, Dana and David Dornsife College of Arts and Sciences, University of Southern California, Los Angeles, California, USA
- Department of Quantitative and Computational Biology, Dana and David Dornsife College of Arts and Sciences, University of Southern California, Los Angeles, California, USA
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Joshi A, Li H, Parikh NA, He L. A systematic review of automated methods to perform white matter tract segmentation. Front Neurosci 2024; 18:1376570. [PMID: 38567281 PMCID: PMC10985163 DOI: 10.3389/fnins.2024.1376570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 03/04/2024] [Indexed: 04/04/2024] Open
Abstract
White matter tract segmentation is a pivotal research area that leverages diffusion-weighted magnetic resonance imaging (dMRI) for the identification and mapping of individual white matter tracts and their trajectories. This study aims to provide a comprehensive systematic literature review on automated methods for white matter tract segmentation in brain dMRI scans. Articles on PubMed, ScienceDirect [NeuroImage, NeuroImage (Clinical), Medical Image Analysis], Scopus and IEEEXplore databases and Conference proceedings of Medical Imaging Computing and Computer Assisted Intervention Society (MICCAI) and International Symposium on Biomedical Imaging (ISBI), were searched in the range from January 2013 until September 2023. This systematic search and review identified 619 articles. Adhering to the specified search criteria using the query, "white matter tract segmentation OR fiber tract identification OR fiber bundle segmentation OR tractography dissection OR white matter parcellation OR tract segmentation," 59 published studies were selected. Among these, 27% employed direct voxel-based methods, 25% applied streamline-based clustering methods, 20% used streamline-based classification methods, 14% implemented atlas-based methods, and 14% utilized hybrid approaches. The paper delves into the research gaps and challenges associated with each of these categories. Additionally, this review paper illuminates the most frequently utilized public datasets for tract segmentation along with their specific characteristics. Furthermore, it presents evaluation strategies and their key attributes. The review concludes with a detailed discussion of the challenges and future directions in this field.
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Affiliation(s)
- Ankita Joshi
- Imaging Research Center, Department of Radiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
- Neurodevelopmental Disorders Prevention Center, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Hailong Li
- Imaging Research Center, Department of Radiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
- Neurodevelopmental Disorders Prevention Center, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
- Department of Radiology, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Nehal A. Parikh
- Neurodevelopmental Disorders Prevention Center, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Lili He
- Imaging Research Center, Department of Radiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
- Neurodevelopmental Disorders Prevention Center, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
- Department of Radiology, University of Cincinnati College of Medicine, Cincinnati, OH, United States
- Computer Science, Biomedical Informatics, and Biomedical Engineering, University of Cincinnati, Cincinnati, OH, United States
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González Rodríguez LL, Osorio I, Cofre G. A, Hernandez Larzabal H, Román C, Poupon C, Mangin JF, Hernández C, Guevara P. Phybers: a package for brain tractography analysis. Front Neurosci 2024; 18:1333243. [PMID: 38529266 PMCID: PMC10962387 DOI: 10.3389/fnins.2024.1333243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 02/09/2024] [Indexed: 03/27/2024] Open
Abstract
We present a Python library (Phybers) for analyzing brain tractography data. Tractography datasets contain streamlines (also called fibers) composed of 3D points representing the main white matter pathways. Several algorithms have been proposed to analyze this data, including clustering, segmentation, and visualization methods. The manipulation of tractography data is not straightforward due to the geometrical complexity of the streamlines, the file format, and the size of the datasets, which may contain millions of fibers. Hence, we collected and structured state-of-the-art methods for the analysis of tractography and packed them into a Python library, to integrate and share tools for tractography analysis. Due to the high computational requirements, the most demanding modules were implemented in C/C++. Available functions include brain Bundle Segmentation (FiberSeg), Hierarchical Fiber Clustering (HClust), Fast Fiber Clustering (FFClust), normalization to a reference coordinate system, fiber sampling, calculation of intersection between sets of brain fibers, tools for cluster filtering, calculation of measures from clusters, and fiber visualization. The library tools were structured into four principal modules: Segmentation, Clustering, Utils, and Visualization (Fibervis). Phybers is freely available on a GitHub repository under the GNU public license for non-commercial use and open-source development, which provides sample data and extensive documentation. In addition, the library can be easily installed on both Windows and Ubuntu operating systems through the pip library.
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Affiliation(s)
| | - Ignacio Osorio
- Department of Electrical Engineering, Faculty of Engineering, Universidad de Concepción, Concepción, Chile
| | - Alejandro Cofre G.
- Department of Electrical Engineering, Faculty of Engineering, Universidad de Concepción, Concepción, Chile
| | - Hernan Hernandez Larzabal
- Department of Electrical Engineering, Faculty of Engineering, Universidad de Concepción, Concepción, Chile
- Latin American Brain Health Institute (BrainLat), Universidad Adolfo Ibañez, Santiago, Chile
| | - Claudio Román
- Centro de Investigación y Desarrollo en Ingeniería en Salud, Universidad de Valparaíso, Valparaíso, Chile
| | - Cyril Poupon
- CEA, CNRS, Baobab, Neurospin, Université Paris-Saclay, Gif-sur-Yvette, France
| | | | - Cecilia Hernández
- Department of Computer Science, Faculty of Engineering, Universidad de Concepción, Concepción, Chile
- Center for Biotechnology and Bioengineering (CeBiB), Santiago, Chile
| | - Pamela Guevara
- Department of Electrical Engineering, Faculty of Engineering, Universidad de Concepción, Concepción, Chile
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Young F, Aquilina K, Seunarine KK, Mancini L, Clark CA, Clayden JD. Fibre orientation atlas guided rapid segmentation of white matter tracts. Hum Brain Mapp 2024; 45:e26578. [PMID: 38339907 PMCID: PMC10826637 DOI: 10.1002/hbm.26578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 12/14/2023] [Accepted: 12/19/2023] [Indexed: 02/12/2024] Open
Abstract
Fibre tract delineation from diffusion magnetic resonance imaging (MRI) is a valuable clinical tool for neurosurgical planning and navigation, as well as in research neuroimaging pipelines. Several popular methods are used for this task, each with different strengths and weaknesses making them more or less suited to different contexts. For neurosurgical imaging, priorities include ease of use, computational efficiency, robustness to pathology and ability to generalise to new tracts of interest. Many existing methods use streamline tractography, which may require expert neuroimaging operators for setting parameters and delineating anatomical regions of interest, or suffer from as a lack of generalisability to clinical scans involving deforming tumours and other pathologies. More recently, data-driven approaches including deep-learning segmentation models and streamline clustering methods have improved reproducibility and automation, although they can require large amounts of training data and/or computationally intensive image processing at the point of application. We describe an atlas-based direct tract mapping technique called 'tractfinder', utilising tract-specific location and orientation priors. Our aim was to develop a clinically practical method avoiding streamline tractography at the point of application while utilising prior anatomical knowledge derived from only 10-20 training samples. Requiring few training samples allows emphasis to be placed on producing high quality, neuro-anatomically accurate training data, and enables rapid adaptation to new tracts of interest. Avoiding streamline tractography at the point of application reduces computational time, false positives and vulnerabilities to pathology such as tumour deformations or oedema. Carefully filtered training streamlines and track orientation distribution mapping are used to construct tract specific orientation and spatial probability atlases in standard space. Atlases are then transformed to target subject space using affine registration and compared with the subject's voxel-wise fibre orientation distribution data using a mathematical measure of distribution overlap, resulting in a map of the tract's likely spatial distribution. This work includes extensive performance evaluation and comparison with benchmark techniques, including streamline tractography and the deep-learning method TractSeg, in two publicly available healthy diffusion MRI datasets (from TractoInferno and the Human Connectome Project) in addition to a clinical dataset comprising paediatric and adult brain tumour scans. Tract segmentation results display high agreement with established techniques while requiring less than 3 min on average when applied to a new subject. Results also display higher robustness than compared methods when faced with clinical scans featuring brain tumours and resections. As well as describing and evaluating a novel proposed tract delineation technique, this work continues the discussion on the challenges surrounding the white matter segmentation task, including issues of anatomical definitions and the use of quantitative segmentation comparison metrics.
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Affiliation(s)
- Fiona Young
- Developmental Neurosciences Research and Teaching Department, UCL Great Ormond Street Institute of Child HealthUniversity College LondonLondonUK
- Department of Medical Physics and Biomedical EngineeringUniversity College LondonLondonUK
| | - Kristian Aquilina
- Department of NeurosurgeryGreat Ormond Street Hospital for ChildrenLondonUK
| | - Kiran K. Seunarine
- Developmental Neurosciences Research and Teaching Department, UCL Great Ormond Street Institute of Child HealthUniversity College LondonLondonUK
- Department of RadiologyGreat Ormond Street Hospital for ChildrenLondonUK
| | - Laura Mancini
- Lysholm Department of Neuroradiology, The National Hospital for Neurology and NeurosurgeryUniversity College London Hospitals NHS Foundation TrustLondonUK
- Department of Brain Repair and Rehabilitation, UCL Queen Square Institute of NeurologyUniversity College LondonLondonUK
| | - Chris A. Clark
- Developmental Neurosciences Research and Teaching Department, UCL Great Ormond Street Institute of Child HealthUniversity College LondonLondonUK
| | - Jonathan D. Clayden
- Developmental Neurosciences Research and Teaching Department, UCL Great Ormond Street Institute of Child HealthUniversity College LondonLondonUK
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Imms P, Chowdhury NF, Chaudhari NN, Amgalan A, Poudel G, Caeyenberghs K, Irimia A. Prediction of cognitive outcome after mild traumatic brain injury from acute measures of communication within brain networks. Cortex 2024; 171:397-412. [PMID: 38103453 PMCID: PMC10922490 DOI: 10.1016/j.cortex.2023.10.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 09/04/2023] [Accepted: 10/20/2023] [Indexed: 12/19/2023]
Abstract
A considerable but ill-defined proportion of patients with mild traumatic brain injury (mTBI) experience persistent cognitive sequelae; the ability to identify such individuals early can help their neurorehabilitation. Here we tested the hypothesis that acute measures of efficient communication within brain networks are associated with patients' risk for unfavorable cognitive outcome six months after mTBI. Diffusion and T1-weighted magnetic resonance imaging, alongside cognitive measures, were obtained to map connectomes both one week and six months post injury in 113 adult patients with mTBI (71 males). For task-related brain networks, communication measures (characteristic path length, global efficiency, navigation efficiency) were moderately correlated with changes in cognition. Taking into account the covariance of age and sex, more unfavorable communication within networks were associated with worse outcomes within cognitive domains frequently impacted by mTBI (episodic and working memory, verbal fluency, inductive reasoning, and processing speed). Individuals with more unfavorable outcomes had significantly longer and less efficient pathways within networks supporting verbal fluency (all t > 2.786, p < .006), highlighting the vulnerability of language to mTBI. Participants in whom a task-related network was relatively inefficient one week post injury were up to eight times more likely to have unfavorable cognitive outcome pertaining to that task. Our findings suggest that communication measures within task-related networks identify mTBI patients who are unlikely to develop persistent cognitive deficits after mTBI. Our approach and findings can help to stratify mTBI patients according to their expected need for follow-up and/or neurorehabilitation.
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Affiliation(s)
- Phoebe Imms
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA USA.
| | - Nahian F Chowdhury
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA USA.
| | - Nikhil N Chaudhari
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA USA; Corwin D. Denney Research Center, Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA USA.
| | - Anar Amgalan
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA USA.
| | - Govinda Poudel
- Mary Mackillop Institute for Health Research, Australian Catholic University, Melbourne, Australia.
| | - Karen Caeyenberghs
- Cognitive Neuroscience Unit, School of Psychology, Deakin University, Melbourne Burwood Campus, Burwood, VIC, Australia.
| | - Andrei Irimia
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA USA; Corwin D. Denney Research Center, Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA USA; Department of Quantitative & Computational Biology, Dana and David Dornsife College of Arts & Sciences, University of Southern California, Los Angeles, CA USA.
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Zeng Q, Yu J, Hu Q, Yin K, Li Q, Huang J, Xie L, Wang J, Zhang C, Wang J, Zhang J, Feng Y. Investigation into white matter microstructure differences in visual training by using an automated fiber tract subclassification segmentation quantification method. Neurosci Lett 2024; 821:137574. [PMID: 38036084 DOI: 10.1016/j.neulet.2023.137574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/25/2023] [Accepted: 11/27/2023] [Indexed: 12/02/2023]
Abstract
Visual training has emerged as a useful framework for investigating training-related brain plasticity, a highly complex task involving the interaction of visual orientation, attention, reasoning, and cognitive functions. However, the effects of long-term visual training on microstructural changes within white matter (WM) is poorly understood. Therefore, a set of visual training programs was designed, and automated fiber tract subclassification segmentation quantification based on diffusion magnetic resonance imaging was performed to obtain the anatomical changes in the brains of visual trainees. First, 40 healthy matched participants were randomly assigned to the training group or the control group. The training group underwent 10 consecutive weeks of visual training. Then, the fiber tracts of the subjects were automatically identified and further classified into fiber clusters to determine the differences between the two groups on a detailed scale. Next, each fiber cluster was divided into segments that can analyze specific areas of a fiber cluster. Lastly, the diffusion metrics of the two groups were comparatively analyzed to delineate the effects of visual training on WM microstructure. Our results showed that there were significant differences in the fiber clusters of the cingulate bundle, thalamus frontal, uncinate fasciculus, and corpus callosum between the training group compared and the control group. In addition, the training group exhibited lower mean fractional anisotropy, higher mean diffusivity and radial diffusivity than the control group. Therefore, the long-term cognitive activities, such as visual training, may systematically influence the WM properties of cognition, attention, memory, and processing speed.
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Affiliation(s)
- Qingrun Zeng
- Institute of Information Processing and Automation, College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China; Zhejiang Provincial United Key Laboratory of Embedded Systems, Hangzhou 310023, China
| | - Jiangli Yu
- Institute of Information Processing and Automation, College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China; Zhejiang Provincial United Key Laboratory of Embedded Systems, Hangzhou 310023, China
| | - Qiming Hu
- Institute of Information Processing and Automation, College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China; Zhejiang Provincial United Key Laboratory of Embedded Systems, Hangzhou 310023, China
| | - Kuiying Yin
- Nanjing Research Institute of Electronic Technology, Nanjing 210012, China
| | - Qixue Li
- Nanjing Research Institute of Electronic Technology, Nanjing 210012, China
| | - Jiahao Huang
- Institute of Information Processing and Automation, College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China; Zhejiang Provincial United Key Laboratory of Embedded Systems, Hangzhou 310023, China
| | - Lei Xie
- Institute of Information Processing and Automation, College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China; Zhejiang Provincial United Key Laboratory of Embedded Systems, Hangzhou 310023, China
| | - Jingqiang Wang
- Institute of Information Processing and Automation, College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China; Zhejiang Provincial United Key Laboratory of Embedded Systems, Hangzhou 310023, China
| | - Chengzhe Zhang
- Institute of Information Processing and Automation, College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China; Zhejiang Provincial United Key Laboratory of Embedded Systems, Hangzhou 310023, China
| | - Jiafeng Wang
- Institute of Information Processing and Automation, College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China; Zhejiang Provincial United Key Laboratory of Embedded Systems, Hangzhou 310023, China
| | - Jiawei Zhang
- Institute of Information Processing and Automation, College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China; Zhejiang Provincial United Key Laboratory of Embedded Systems, Hangzhou 310023, China
| | - Yuanjing Feng
- Institute of Information Processing and Automation, College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China; Zhejiang Provincial United Key Laboratory of Embedded Systems, Hangzhou 310023, China.
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Meesters S, Landers M, Rutten GJ, Florack L. Subject-Specific Automatic Reconstruction of White Matter Tracts. J Digit Imaging 2023; 36:2648-2661. [PMID: 37537513 PMCID: PMC10584769 DOI: 10.1007/s10278-023-00883-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 07/05/2023] [Accepted: 07/05/2023] [Indexed: 08/05/2023] Open
Abstract
MRI-based tractography is still underexploited and unsuited for routine use in brain tumor surgery due to heterogeneity of methods and functional-anatomical definitions and above all, the lack of a turn-key system. Standardization of methods is therefore desirable, whereby an objective and reliable approach is a prerequisite before the results of any automated procedure can subsequently be validated and used in neurosurgical practice. In this work, we evaluated these preliminary but necessary steps in healthy volunteers. Specifically, we evaluated the robustness and reliability (i.e., test-retest reproducibility) of tractography results of six clinically relevant white matter tracts by using healthy volunteer data (N = 136) from the Human Connectome Project consortium. A deep learning convolutional network-based approach was used for individualized segmentation of regions of interest, combined with an evidence-based tractography protocol and appropriate post-tractography filtering. Robustness was evaluated by estimating the consistency of tractography probability maps, i.e., averaged tractograms in normalized space, through the use of a hold-out cross-validation approach. No major outliers were found, indicating a high robustness of the tractography results. Reliability was evaluated at the individual level. First by examining the overlap of tractograms that resulted from repeatedly processed identical MRI scans (N = 10, 10 iterations) to establish an upper limit of reliability of the pipeline. Second, by examining the overlap for subjects that were scanned twice at different time points (N = 40). Both analyses indicated high reliability, with the second analysis showing a reliability near the upper limit. The robust and reliable subject-specific generation of white matter tracts in healthy subjects holds promise for future validation of our pipeline in a clinical population and subsequent implementation in brain tumor surgery.
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Affiliation(s)
- Stephan Meesters
- Department of Mathematics & Computer Science, Eindhoven University of Technology, Eindhoven, The Netherlands
- Department of Neurosurgery, Elisabeth-Tweesteden Hospital, Tilburg, The Netherlands
| | - Maud Landers
- Department of Neurosurgery, Elisabeth-Tweesteden Hospital, Tilburg, The Netherlands
| | - Geert-Jan Rutten
- Department of Neurosurgery, Elisabeth-Tweesteden Hospital, Tilburg, The Netherlands.
| | - Luc Florack
- Department of Mathematics & Computer Science, Eindhoven University of Technology, Eindhoven, The Netherlands
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Lucena O, Lavrador JP, Irzan H, Semedo C, Borges P, Vergani F, Granados A, Sparks R, Ashkan K, Ourselin S. Assessing informative tract segmentation and nTMS for pre-operative planning. J Neurosci Methods 2023; 396:109933. [PMID: 37524245 PMCID: PMC10861808 DOI: 10.1016/j.jneumeth.2023.109933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/15/2023] [Accepted: 07/28/2023] [Indexed: 08/02/2023]
Abstract
BACKGROUND Deep learning-based (DL) methods are the best-performing methods for white matter tract segmentation in anatomically healthy subjects. However, tract annotations are variable or absent in clinical data and manual annotations are especially difficult in patients with tumors where normal anatomy may be distorted. Direct cortical and subcortical stimulation is the gold standard ground truth to determine the cortical and sub-cortical lo- cation of motor-eloquent areas intra-operatively. Nonetheless, this technique is invasive, prolongs the surgical procedure, and may cause patient fatigue. Navigated Transcranial Magnetic Stimulation (nTMS) has a well-established correlation to direct cortical stimulation for motor mapping and the added advantage of being able to be acquired pre-operatively. NEW METHOD In this work, we evaluate the feasibility of using nTMS motor responses as a method to assess corticospinal tract (CST) binary masks and estimated uncertainty generated by a DL-based tract segmentation in patients with diffuse gliomas. RESULTS Our results show CST binary masks have a high overlap coefficient (OC) with nTMS response masks. A strong negative correlation is found between estimated uncertainty and nTMS response mask distance to the CST binary mask. COMPARISON WITH EXISTING METHODS We compare our approach (UncSeg) with the state-of-the-art TractSeg in terms of OC between the CST binary masks and nTMS response masks. CONCLUSIONS In this study, we demonstrate that estimated uncertainty from UncSeg is a good measure of the agreement between the CST binary masks and nTMS response masks distance to the CST binary mask boundary.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Keyoumars Ashkan
- King's College London, London, UK; King's College Hospital Foundation Trust, London, UK
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Shams B, Reisch K, Vajkoczy P, Lippert C, Picht T, Fekonja LS. Improved prediction of glioma-related aphasia by diffusion MRI metrics, machine learning, and automated fiber bundle segmentation. Hum Brain Mapp 2023. [PMID: 37318944 PMCID: PMC10365236 DOI: 10.1002/hbm.26393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/07/2023] [Accepted: 05/26/2023] [Indexed: 06/17/2023] Open
Abstract
White matter impairments caused by gliomas can lead to functional disorders. In this study, we predicted aphasia in patients with gliomas infiltrating the language network using machine learning methods. We included 78 patients with left-hemispheric perisylvian gliomas. Aphasia was graded preoperatively using the Aachen aphasia test (AAT). Subsequently, we created bundle segmentations based on automatically generated tract orientation mappings using TractSeg. To prepare the input for the support vector machine (SVM), we first preselected aphasia-related fiber bundles based on the associations between relative tract volumes and AAT subtests. In addition, diffusion magnetic resonance imaging (dMRI)-based metrics [axial diffusivity (AD), apparent diffusion coefficient (ADC), fractional anisotropy (FA), and radial diffusivity (RD)] were extracted within the fiber bundles' masks with their mean, standard deviation, kurtosis, and skewness values. Our model consisted of random forest-based feature selection followed by an SVM. The best model performance achieved 81% accuracy (specificity = 85%, sensitivity = 73%, and AUC = 85%) using dMRI-based features, demographics, tumor WHO grade, tumor location, and relative tract volumes. The most effective features resulted from the arcuate fasciculus (AF), middle longitudinal fasciculus (MLF), and inferior fronto-occipital fasciculus (IFOF). The most effective dMRI-based metrics were FA, ADC, and AD. We achieved a prediction of aphasia using dMRI-based features and demonstrated that AF, IFOF, and MLF were the most important fiber bundles for predicting aphasia in this cohort.
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Affiliation(s)
- Boshra Shams
- Department of Neurosurgery, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Cluster of Excellence: "Matters of Activity. Image Space Material", Humboldt University, Berlin, Germany
| | - Klara Reisch
- Department of Neurosurgery, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Peter Vajkoczy
- Department of Neurosurgery, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Christoph Lippert
- Digital Health - Machine Learning, Hasso Plattner Institute, University of Potsdam, Digital Engineering Faculty, Potsdam, Germany
- Hasso Plattner Institute for Digital Health, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Thomas Picht
- Department of Neurosurgery, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Cluster of Excellence: "Matters of Activity. Image Space Material", Humboldt University, Berlin, Germany
| | - Lucius S Fekonja
- Department of Neurosurgery, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Cluster of Excellence: "Matters of Activity. Image Space Material", Humboldt University, Berlin, Germany
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10
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Levitt JJ, Zhang F, Vangel M, Nestor PG, Rathi Y, Cetin-Karayumak S, Kubicki M, Coleman MJ, Lewandowski KE, Holt DJ, Keshavan M, Bouix S, Öngür D, Breier A, Shenton ME, O'Donnell LJ. The organization of frontostriatal brain wiring in non-affective early psychosis compared with healthy subjects using a novel diffusion imaging fiber cluster analysis. Mol Psychiatry 2023; 28:2301-2311. [PMID: 37173451 DOI: 10.1038/s41380-023-02031-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 02/13/2023] [Accepted: 03/08/2023] [Indexed: 05/15/2023]
Abstract
BACKGROUND Alterations in brain connectivity may underlie neuropsychiatric conditions such as schizophrenia. We here assessed the degree of convergence of frontostriatal fiber projections in 56 young adult healthy controls (HCs) and 108 matched Early Psychosis-Non-Affective patients (EP-NAs) using our novel fiber cluster analysis of whole brain diffusion magnetic resonance imaging tractography. METHODS Using whole brain tractography and our fiber clustering methodology on harmonized diffusion magnetic resonance imaging data from the Human Connectome Project for Early Psychosis we identified 17 white matter fiber clusters that connect frontal cortex (FCtx) and caudate (Cd) per hemisphere in each group. To quantify the degree of convergence and, hence, topographical relationship of these fiber clusters, we measured the inter-cluster mean distances between the endpoints of the fiber clusters at the level of the FCtx and of the Cd, respectively. RESULTS We found (1) in both groups, bilaterally, a non-linear relationship, yielding convex curves, between FCtx and Cd distances for FCtx-Cd connecting fiber clusters, driven by a cluster projecting from inferior frontal gyrus; however, in the right hemisphere, the convex curve was more flattened in EP-NAs; (2) that cluster pairs in the right (p = 0.03), but not left (p = 0.13), hemisphere were significantly more convergent in HCs vs EP-NAs; (3) in both groups, bilaterally, similar clusters projected significantly convergently to the Cd; and, (4) a significant group by fiber cluster pair interaction for 2 right hemisphere fiber clusters (numbers 5, 11; p = .00023; p = .00023) originating in selective PFC subregions. CONCLUSIONS In both groups, we found the FCtx-Cd wiring pattern deviated from a strictly topographic relationship and that similar clusters projected significantly more convergently to the Cd. Interestingly, we also found a significantly more convergent pattern of connectivity in HCs in the right hemisphere and that 2 clusters from PFC subregions in the right hemisphere significantly differed in their pattern of connectivity between groups.
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Affiliation(s)
- J J Levitt
- Department of Psychiatry, VA Boston Healthcare System, Brockton Division, Brockton, MA, 02301, USA.
- Harvard Medical School, Boston, MA, 02115, USA.
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
| | - F Zhang
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - M Vangel
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - P G Nestor
- Department of Psychiatry, VA Boston Healthcare System, Brockton Division, Brockton, MA, 02301, USA
- Harvard Medical School, Boston, MA, 02115, USA
- Department of Psychology, University of Massachusetts, Boston, MA, 02125, USA
| | - Y Rathi
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - S Cetin-Karayumak
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - M Kubicki
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - M J Coleman
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - K E Lewandowski
- McLean Hospital, Harvard Medical School, Belmont, MA, 02478, USA
| | - D J Holt
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - M Keshavan
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - S Bouix
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Department of Software Engineering and Information Technology, École de technologie supérieure, Université du Québec, Montréal, QC, H3C 1K3, Canada
| | - D Öngür
- McLean Hospital, Harvard Medical School, Belmont, MA, 02478, USA
| | - A Breier
- Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - M E Shenton
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - L J O'Donnell
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
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11
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Chen Y, Zhang C, Xue T, Song Y, Makris N, Rathi Y, Cai W, Zhang F, O'Donnell LJ. Deep fiber clustering: Anatomically informed fiber clustering with self-supervised deep learning for fast and effective tractography parcellation. Neuroimage 2023; 273:120086. [PMID: 37019346 PMCID: PMC10958986 DOI: 10.1016/j.neuroimage.2023.120086] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/02/2023] [Indexed: 04/05/2023] Open
Abstract
White matter fiber clustering is an important strategy for white matter parcellation, which enables quantitative analysis of brain connections in health and disease. In combination with expert neuroanatomical labeling, data-driven white matter fiber clustering is a powerful tool for creating atlases that can model white matter anatomy across individuals. While widely used fiber clustering approaches have shown good performance using classical unsupervised machine learning techniques, recent advances in deep learning reveal a promising direction toward fast and effective fiber clustering. In this work, we propose a novel deep learning framework for white matter fiber clustering, Deep Fiber Clustering (DFC), which solves the unsupervised clustering problem as a self-supervised learning task with a domain-specific pretext task to predict pairwise fiber distances. This process learns a high-dimensional embedding feature representation for each fiber, regardless of the order of fiber points reconstructed during tractography. We design a novel network architecture that represents input fibers as point clouds and allows the incorporation of additional sources of input information from gray matter parcellation. Thus, DFC makes use of combined information about white matter fiber geometry and gray matter anatomy to improve the anatomical coherence of fiber clusters. In addition, DFC conducts outlier removal naturally by rejecting fibers with low cluster assignment probability. We evaluate DFC on three independently acquired cohorts, including data from 220 individuals across genders, ages (young and elderly adults), and different health conditions (healthy control and multiple neuropsychiatric disorders). We compare DFC to several state-of-the-art white matter fiber clustering algorithms. Experimental results demonstrate superior performance of DFC in terms of cluster compactness, generalization ability, anatomical coherence, and computational efficiency.
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Affiliation(s)
- Yuqian Chen
- Harvard Medical School, MA, USA; The University of Sydney, NSW, Australia
| | | | - Tengfei Xue
- Harvard Medical School, MA, USA; The University of Sydney, NSW, Australia
| | - Yang Song
- The University of New South Wales, NSW, Australia
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12
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Langhein M, Lyall AE, Steinmann S, Seitz-Holland J, Nägele FL, Cetin-Karayumak S, Zhang F, Rauh J, Mußmann M, Billah T, Makris N, Pasternak O, O’Donnell LJ, Rathi Y, Leicht G, Kubicki M, Shenton ME, Mulert C. The decoupling of structural and functional connectivity of auditory networks in individuals at clinical high-risk for psychosis. World J Biol Psychiatry 2023; 24:387-399. [PMID: 36083108 PMCID: PMC10399965 DOI: 10.1080/15622975.2022.2112974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 10/14/2022]
Abstract
OBJECTIVES Disrupted auditory networks play an important role in the pathophysiology of psychosis, with abnormalities already observed in individuals at clinical high-risk for psychosis (CHR). Here, we examine structural and functional connectivity of an auditory network in CHR utilising state-of-the-art electroencephalography and diffusion imaging techniques. METHODS Twenty-six CHR subjects and 13 healthy controls (HC) underwent diffusion MRI and electroencephalography while performing an auditory task. We investigated structural connectivity, measured as fractional anisotropy in the Arcuate Fasciculus (AF), Cingulum Bundle, and Superior Longitudinal Fasciculus-II. Gamma-band lagged-phase synchronisation, a functional connectivity measure, was calculated between cortical regions connected by these tracts. RESULTS CHR subjects showed significantly higher structural connectivity in the right AF than HC (p < .001). Although non-significant, functional connectivity between cortical areas connected by the AF was lower in CHR than HC (p = .078). Structural and functional connectivity were correlated in HC (p = .056) but not in CHR (p = .29). CONCLUSIONS We observe significant differences in structural connectivity of the AF, without a concomitant significant change in functional connectivity in CHR subjects. This may suggest that the CHR state is characterised by a decoupling of structural and functional connectivity, possibly due to abnormal white matter maturation.
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Affiliation(s)
- Mina Langhein
- Psychiatry Neuroimaging Branch, Department of Psychiatry and Psychotherapy, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Amanda E. Lyall
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Saskia Steinmann
- Psychiatry Neuroimaging Branch, Department of Psychiatry and Psychotherapy, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Johanna Seitz-Holland
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Felix L. Nägele
- Psychiatry Neuroimaging Branch, Department of Psychiatry and Psychotherapy, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Suheyla Cetin-Karayumak
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Fan Zhang
- Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Jonas Rauh
- Psychiatry Neuroimaging Branch, Department of Psychiatry and Psychotherapy, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marius Mußmann
- Psychiatry Neuroimaging Branch, Department of Psychiatry and Psychotherapy, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tashrif Billah
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Nikos Makris
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ofer Pasternak
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Lauren J O’Donnell
- Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Yogesh Rathi
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Gregor Leicht
- Psychiatry Neuroimaging Branch, Department of Psychiatry and Psychotherapy, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marek Kubicki
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Martha E. Shenton
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Christoph Mulert
- Psychiatry Neuroimaging Branch, Department of Psychiatry and Psychotherapy, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Centre for Psychiatry, Justus-Liebig-University, Giessen, Germany
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13
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Sullivan JJ, Zekelman LR, Zhang F, Juvekar P, Torio EF, Bunevicius A, Essayed WI, Bastos D, He J, Rigolo L, Golby AJ, O'Donnell LJ. Directionally encoded color track density imaging in brain tumor patients: A potential application to neuro-oncology surgical planning. Neuroimage Clin 2023; 38:103412. [PMID: 37116355 PMCID: PMC10165166 DOI: 10.1016/j.nicl.2023.103412] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/01/2023] [Accepted: 04/17/2023] [Indexed: 04/30/2023]
Abstract
BACKGROUND Diffusion magnetic resonance imaging white matter tractography, an increasingly popular preoperative planning modality used for pre-surgical planning in brain tumor patients, is employed with the goal of maximizing tumor resection while sparing postoperative neurological function. Clinical translation of white matter tractography has been limited by several shortcomings of standard diffusion tensor imaging (DTI), including poor modeling of fibers crossing through regions of peritumoral edema and low spatial resolution for typical clinical diffusion MRI (dMRI) sequences. Track density imaging (TDI) is a post-tractography technique that uses the number of tractography streamlines and their long-range continuity to map the white matter connections of the brain with enhanced image resolution relative to the acquired dMRI data, potentially offering improved white matter visualization in patients with brain tumors. The aim of this study was to assess the utility of TDI-based white matter maps in a neurosurgical planning context compared to the current clinical standard of DTI-based white matter maps. METHODS Fourteen consecutive brain tumor patients from a single institution were retrospectively selected for the study. Each patient underwent 3-Tesla dMRI scanning with 30 gradient directions and a b-value of 1000 s/mm2. For each patient, two directionally encoded color (DEC) maps were produced as follows. DTI-based DEC-fractional anisotropy maps (DEC-FA) were generated on the scanner, while DEC-track density images (DEC-TDI) were generated using constrained spherical deconvolution based tractography. The potential clinical utility of each map was assessed by five practicing neurosurgeons, who rated the maps according to four clinical utility statements regarding different clinical aspects of pre-surgical planning. The neurosurgeons rated each map according to their agreement with four clinical utility statements regarding if the map 1 identified clinically relevant tracts, (2) helped establish a goal resection margin, (3) influenced a planned surgical route, and (4) was useful overall. Cumulative link mixed effect modeling and analysis of variance were performed to test the primary effect of map type (DEC-TDI vs. DEC-FA) on rater score. Pairwise comparisons using estimated marginal means were then calculated to determine the magnitude and directionality of differences in rater scores by map type. RESULTS A majority of rater responses agreed with the four clinical utility statements, indicating that neurosurgeons found both DEC maps to be useful. Across all four investigated clinical utility statements, the DEC map type significantly influenced rater score. Rater scores were significantly higher for DEC-TDI maps compared to DEC-FA maps. The largest effect size in rater scores in favor of DEC-TDI maps was observed for clinical utility statement 2, which assessed establishing a goal resection margin. CONCLUSION We observed a significant neurosurgeon preference for DEC-TDI maps, indicating their potential utility for neurosurgical planning.
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Affiliation(s)
- Jared J Sullivan
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis St., Boston, MA 02115, United States; Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, 60 Fenwood Rd., Boston, MA 02115, United States
| | - Leo R Zekelman
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, 60 Fenwood Rd., Boston, MA 02115, United States
| | - Fan Zhang
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis St., Boston, MA 02115, United States
| | - Parikshit Juvekar
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, 60 Fenwood Rd., Boston, MA 02115, United States
| | - Erickson F Torio
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, 60 Fenwood Rd., Boston, MA 02115, United States
| | - Adomas Bunevicius
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, 60 Fenwood Rd., Boston, MA 02115, United States
| | - Walid I Essayed
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, 60 Fenwood Rd., Boston, MA 02115, United States
| | - Dhiego Bastos
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, 60 Fenwood Rd., Boston, MA 02115, United States
| | - Jianzhong He
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis St., Boston, MA 02115, United States
| | - Laura Rigolo
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, 60 Fenwood Rd., Boston, MA 02115, United States
| | - Alexandra J Golby
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis St., Boston, MA 02115, United States; Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, 60 Fenwood Rd., Boston, MA 02115, United States
| | - Lauren J O'Donnell
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis St., Boston, MA 02115, United States.
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14
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Umminger LF, Rojczyk P, Seitz-Holland J, Sollmann N, Kaufmann E, Kinzel P, Zhang F, Kochsiek J, Langhein M, Kim CL, Wiegand TLT, Kilts JD, Naylor JC, Grant GA, Rathi Y, Coleman MJ, Bouix S, Tripodis Y, Pasternak O, George MS, McAllister TW, Zafonte R, Stein MB, O'Donnell LJ, Marx CE, Shenton ME, Koerte IK. White Matter Microstructure Is Associated with Serum Neuroactive Steroids and Psychological Functioning. J Neurotrauma 2023; 40:649-664. [PMID: 36324218 PMCID: PMC10061338 DOI: 10.1089/neu.2022.0111] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Military service members are at increased risk for mental health issues, and comorbidity with mild traumatic brain injury (mTBI) is common. Largely overlapping symptoms between conditions suggest a shared pathophysiology. The present work investigates the associations among white matter microstructure, psychological functioning, and serum neuroactive steroids that are part of the stress-response system. Diffusion-weighted brain imaging was acquired from 163 participants (with and without military affiliation) and free-water-corrected fractional anisotropy (FAT) was extracted. Associations between serum neurosteroid levels of allopregnanolone (ALLO) and pregnenolone (PREGNE), psychological functioning, and whole-brain white matter microstructure were assessed using regression models. Moderation models tested the effect of mTBI and comorbid post-traumatic stress disorder (PTSD) and mTBI on these associations. ALLO is associated with whole-brain white matter FAT (β = 0.24, t = 3.05, p = 0.006). This association is significantly modulated by PTSD+mTBI comorbidity (β = 0.00, t = 2.50, p = 0.027), although an mTBI diagnosis alone did not significantly impact this association (p = 0.088). There was no significant association between PREGNE and FAT (p = 0.380). Importantly, lower FAT is associated with poor psychological functioning (β = -0.19, t = -2.35, p = 0.020). This study provides novel insight into a potential common pathophysiological mechanism of neurosteroid dysregulation underlying the high risk for mental health issues in military service members. Further, comorbidity of PTSD and mTBI may bring the compensatory effects of the brain's stress response to their limit. Future research is needed to investigate whether neurosteroid regulation may be a promising tool for restoring brain health and improving psychological functioning.
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Affiliation(s)
- Lisa F. Umminger
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- cBRAIN, Department of Child and Adolescent Psychiatry, Psychosomatic and Psychotherapy, Ludwig-Maximilians-Universität, Munich, Germany
| | - Philine Rojczyk
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- cBRAIN, Department of Child and Adolescent Psychiatry, Psychosomatic and Psychotherapy, Ludwig-Maximilians-Universität, Munich, Germany
| | - Johanna Seitz-Holland
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Nico Sollmann
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- cBRAIN, Department of Child and Adolescent Psychiatry, Psychosomatic and Psychotherapy, Ludwig-Maximilians-Universität, Munich, Germany
- Department of Diagnostic and Interventional Radiology, University Hospital Ulm, Ulm, Germany
- Department of Diagnostic and Interventional Neuroradiology, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- TUM-Neuroimaging Center, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Elisabeth Kaufmann
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- cBRAIN, Department of Child and Adolescent Psychiatry, Psychosomatic and Psychotherapy, Ludwig-Maximilians-Universität, Munich, Germany
- Department of Neurology, Epilepsy Center, Ludwig-Maximilians-Universität, Munich, Germany
| | - Philipp Kinzel
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- cBRAIN, Department of Child and Adolescent Psychiatry, Psychosomatic and Psychotherapy, Ludwig-Maximilians-Universität, Munich, Germany
| | - Fan Zhang
- Laboratory of Mathematics in Imaging, Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Janna Kochsiek
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- cBRAIN, Department of Child and Adolescent Psychiatry, Psychosomatic and Psychotherapy, Ludwig-Maximilians-Universität, Munich, Germany
| | - Mina Langhein
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Cara L. Kim
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- cBRAIN, Department of Child and Adolescent Psychiatry, Psychosomatic and Psychotherapy, Ludwig-Maximilians-Universität, Munich, Germany
| | - Tim L. T. Wiegand
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- cBRAIN, Department of Child and Adolescent Psychiatry, Psychosomatic and Psychotherapy, Ludwig-Maximilians-Universität, Munich, Germany
| | - Jason D. Kilts
- VA Mid-Atlantic Mental Illness Research and Clinical Center (MIRECC) and Durham VA Medical Center, Durham, NorthCarolina, USA
- Department of Psychiatry and Behavior Sciences, Duke University School of Medicine, Durham, North Carolina, USA
| | - Jennifer C. Naylor
- VA Mid-Atlantic Mental Illness Research and Clinical Center (MIRECC) and Durham VA Medical Center, Durham, NorthCarolina, USA
- Department of Psychiatry and Behavior Sciences, Duke University School of Medicine, Durham, North Carolina, USA
| | - Gerald A. Grant
- Department of Neurosurgery, Duke University School of Medicine, Durham, North Carolina, USA
| | - Yogesh Rathi
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael J. Coleman
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Sylvain Bouix
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Yorghos Tripodis
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
- Boston University Alzheimer's Disease and CTE Center, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Ofer Pasternak
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Mark S. George
- Psychiatry Department, Medical University of South Carolina, Charleston, South Carolina, USA
- Ralph H. Johnson VA Medical Center, Charleston, South Carolina, USA
| | - Thomas W. McAllister
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Ross Zafonte
- Department of Physical Medicine and Rehabilitation, Spaulding Rehabilitation Hospital, Harvard Medical School, Charlestown, Massachusetts, USA
- Department of Physical Medicine and Rehabilitation, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Murray B. Stein
- Department of Psychiatry, University of California San Diego, La Jolla, California, USA
- School of Public Health, University of California San Diego, La Jolla, California, USA
- Psychiatry Service, VA San Diego Healthcare System, San Diego, CA, USA
| | - Lauren J. O'Donnell
- Laboratory of Mathematics in Imaging, Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Christine E. Marx
- VA Mid-Atlantic Mental Illness Research and Clinical Center (MIRECC) and Durham VA Medical Center, Durham, NorthCarolina, USA
- Department of Psychiatry and Behavior Sciences, Duke University School of Medicine, Durham, North Carolina, USA
| | - Martha E. Shenton
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Inga K. Koerte
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- cBRAIN, Department of Child and Adolescent Psychiatry, Psychosomatic and Psychotherapy, Ludwig-Maximilians-Universität, Munich, Germany
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Graduate School of Systemic Neuroscience, Ludwig-Maximilians-Universität, Munich, Germany
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15
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Xue T, Zhang F, Zhang C, Chen Y, Song Y, Golby AJ, Makris N, Rathi Y, Cai W, O'Donnell LJ. Superficial white matter analysis: An efficient point-cloud-based deep learning framework with supervised contrastive learning for consistent tractography parcellation across populations and dMRI acquisitions. Med Image Anal 2023; 85:102759. [PMID: 36706638 PMCID: PMC9975054 DOI: 10.1016/j.media.2023.102759] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 01/05/2023] [Accepted: 01/20/2023] [Indexed: 01/24/2023]
Abstract
Diffusion MRI tractography is an advanced imaging technique that enables in vivo mapping of the brain's white matter connections. White matter parcellation classifies tractography streamlines into clusters or anatomically meaningful tracts. It enables quantification and visualization of whole-brain tractography. Currently, most parcellation methods focus on the deep white matter (DWM), whereas fewer methods address the superficial white matter (SWM) due to its complexity. We propose a novel two-stage deep-learning-based framework, Superficial White Matter Analysis (SupWMA), that performs an efficient and consistent parcellation of 198 SWM clusters from whole-brain tractography. A point-cloud-based network is adapted to our SWM parcellation task, and supervised contrastive learning enables more discriminative representations between plausible streamlines and outliers for SWM. We train our model on a large-scale tractography dataset including streamline samples from labeled long- and medium-range (over 40 mm) SWM clusters and anatomically implausible streamline samples, and we perform testing on six independently acquired datasets of different ages and health conditions (including neonates and patients with space-occupying brain tumors). Compared to several state-of-the-art methods, SupWMA obtains highly consistent and accurate SWM parcellation results on all datasets, showing good generalization across the lifespan in health and disease. In addition, the computational speed of SupWMA is much faster than other methods.
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Affiliation(s)
- Tengfei Xue
- Brigham and Women's Hospital, Harvard Medical School, Boston, USA; School of Computer Science, University of Sydney, Sydney, Australia
| | - Fan Zhang
- Brigham and Women's Hospital, Harvard Medical School, Boston, USA.
| | - Chaoyi Zhang
- School of Computer Science, University of Sydney, Sydney, Australia
| | - Yuqian Chen
- Brigham and Women's Hospital, Harvard Medical School, Boston, USA; School of Computer Science, University of Sydney, Sydney, Australia
| | - Yang Song
- School of Computer Science and Engineering, University of New South Wales, Sydney, Australia
| | | | - Nikos Makris
- Brigham and Women's Hospital, Harvard Medical School, Boston, USA; Center for Morphometric Analysis, Massachusetts General Hospital, Boston, USA
| | - Yogesh Rathi
- Brigham and Women's Hospital, Harvard Medical School, Boston, USA
| | - Weidong Cai
- School of Computer Science, University of Sydney, Sydney, Australia
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16
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Rojczyk P, Seitz-Holland J, Kaufmann E, Sydnor VJ, Kim CL, Umminger LF, Wiegand TLT, Guenette JP, Zhang F, Rathi Y, Bouix S, Pasternak O, Fortier CB, Salat D, Hinds SR, Heinen F, O’Donnell LJ, Milberg WP, McGlinchey RE, Shenton ME, Koerte IK. Sleep Quality Disturbances Are Associated with White Matter Alterations in Veterans with Post-Traumatic Stress Disorder and Mild Traumatic Brain Injury. J Clin Med 2023; 12:2079. [PMID: 36902865 PMCID: PMC10004675 DOI: 10.3390/jcm12052079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 03/09/2023] Open
Abstract
Sleep disturbances are strongly associated with mild traumatic brain injury (mTBI) and post-traumatic stress disorder (PTSD). PTSD and mTBI have been linked to alterations in white matter (WM) microstructure, but whether poor sleep quality has a compounding effect on WM remains largely unknown. We evaluated sleep and diffusion magnetic resonance imaging (dMRI) data from 180 male post-9/11 veterans diagnosed with (1) PTSD (n = 38), (2) mTBI (n = 25), (3) comorbid PTSD+mTBI (n = 94), and (4) a control group with neither PTSD nor mTBI (n = 23). We compared sleep quality (Pittsburgh Sleep Quality Index, PSQI) between groups using ANCOVAs and calculated regression and mediation models to assess associations between PTSD, mTBI, sleep quality, and WM. Veterans with PTSD and comorbid PTSD+mTBI reported poorer sleep quality than those with mTBI or no history of PTSD or mTBI (p = 0.012 to <0.001). Poor sleep quality was associated with abnormal WM microstructure in veterans with comorbid PTSD+mTBI (p < 0.001). Most importantly, poor sleep quality fully mediated the association between greater PTSD symptom severity and impaired WM microstructure (p < 0.001). Our findings highlight the significant impact of sleep disturbances on brain health in veterans with PTSD+mTBI, calling for sleep-targeted interventions.
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Affiliation(s)
- Philine Rojczyk
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02145, USA
- cBRAIN, Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy, Ludwig-Maximilians-University, 80336 Munich, Germany
| | - Johanna Seitz-Holland
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02145, USA
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Elisabeth Kaufmann
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02145, USA
- cBRAIN, Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy, Ludwig-Maximilians-University, 80336 Munich, Germany
- Department of Neurology, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Valerie J. Sydnor
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02145, USA
| | - Cara L. Kim
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02145, USA
- cBRAIN, Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy, Ludwig-Maximilians-University, 80336 Munich, Germany
| | - Lisa F. Umminger
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02145, USA
- cBRAIN, Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy, Ludwig-Maximilians-University, 80336 Munich, Germany
| | - Tim L. T. Wiegand
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02145, USA
- cBRAIN, Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy, Ludwig-Maximilians-University, 80336 Munich, Germany
| | - Jeffrey P. Guenette
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02145, USA
- Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Fan Zhang
- Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Yogesh Rathi
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02145, USA
- Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sylvain Bouix
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02145, USA
- Department of Software Engineering and IT, École de Technologie Supérieure, Montreal, QC H3C 1K3, Canada
| | - Ofer Pasternak
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02145, USA
- Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Catherine B. Fortier
- Translational Research Center for TBI and Stress Disorders (TRACTS) and Geriatric Research, Education and Clinical Center (GRECC), VA Boston Healthcare System, Boston, MA 02130, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA 02215, USA
| | - David Salat
- Translational Research Center for TBI and Stress Disorders (TRACTS) and Geriatric Research, Education and Clinical Center (GRECC), VA Boston Healthcare System, Boston, MA 02130, USA
- Neuroimaging Research for Veterans (NeRVe) Center, VA Boston Healthcare System, Boston, 02115 MA, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Department of Radiology, Boston, MA 02129, USA
| | - Sidney R. Hinds
- Department of Neurology, Uniformed Services University, Bethesda, MD 20814, USA
| | - Florian Heinen
- Department of Pediatric Neurology and Developmental Medicine and LMU Center for Children with Medical Complexity, Dr. von Hauner Children’s Hospital, Ludwig-Maximilians-University, 80337 Munich, Germany
| | - Lauren J. O’Donnell
- Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - William P. Milberg
- Translational Research Center for TBI and Stress Disorders (TRACTS) and Geriatric Research, Education and Clinical Center (GRECC), VA Boston Healthcare System, Boston, MA 02130, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA 02215, USA
- Neuroimaging Research for Veterans (NeRVe) Center, VA Boston Healthcare System, Boston, 02115 MA, USA
| | - Regina E. McGlinchey
- Translational Research Center for TBI and Stress Disorders (TRACTS) and Geriatric Research, Education and Clinical Center (GRECC), VA Boston Healthcare System, Boston, MA 02130, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA 02215, USA
- Neuroimaging Research for Veterans (NeRVe) Center, VA Boston Healthcare System, Boston, 02115 MA, USA
| | - Martha E. Shenton
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02145, USA
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Inga K. Koerte
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02145, USA
- cBRAIN, Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy, Ludwig-Maximilians-University, 80336 Munich, Germany
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Graduate School of Systemic Neurosciences, Ludwig-Maximilians-University, 82152 Munich, Germany
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17
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Prediction of the Topography of the Corticospinal Tract on T1-Weighted MR Images Using Deep-Learning-Based Segmentation. Diagnostics (Basel) 2023; 13:diagnostics13050911. [PMID: 36900055 PMCID: PMC10000710 DOI: 10.3390/diagnostics13050911] [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: 01/29/2023] [Revised: 02/23/2023] [Accepted: 02/27/2023] [Indexed: 03/04/2023] Open
Abstract
INTRODUCTION Tractography is an invaluable tool in the planning of tumor surgery in the vicinity of functionally eloquent areas of the brain as well as in the research of normal development or of various diseases. The aim of our study was to compare the performance of a deep-learning-based image segmentation for the prediction of the topography of white matter tracts on T1-weighted MR images to the performance of a manual segmentation. METHODS T1-weighted MR images of 190 healthy subjects from 6 different datasets were utilized in this study. Using deterministic diffusion tensor imaging, we first reconstructed the corticospinal tract on both sides. After training a segmentation model on 90 subjects of the PIOP2 dataset using the nnU-Net in a cloud-based environment with graphical processing unit (Google Colab), we evaluated its performance using 100 subjects from 6 different datasets. RESULTS Our algorithm created a segmentation model that predicted the topography of the corticospinal pathway on T1-weighted images in healthy subjects. The average dice score was 0.5479 (0.3513-0.7184) on the validation dataset. CONCLUSIONS Deep-learning-based segmentation could be applicable in the future to predict the location of white matter pathways in T1-weighted scans.
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Zhang C, Yuan Y, Sang T, Yu L, Yu Y, Liu X, Zhou W, Zeng Q, Wang J, Peng G, Feng Y. Local white matter abnormalities in Parkinson's disease with mild cognitive impairment: Assessed with neurite orientation dispersion and density imaging. J Neurosci Res 2023; 101:1154-1169. [PMID: 36854050 DOI: 10.1002/jnr.25179] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 12/06/2022] [Accepted: 01/31/2023] [Indexed: 03/02/2023]
Abstract
Mild cognitive impairment is a nonmotor complication in Parkinson's disease (PD) that have a high risk of developing dementia. White matter is associated with cognitive function in PD and the alterations may occur before the symptoms of the disease. Previous diffusion tensor imaging (DTI) studies lacked specificity to characterize the concrete contributions of distinct white matter tissue properties. This may lead to inconsistent conclusions about the alteration of white matter microstructure. Here, we used neurite orientation dispersion and density imaging (NODDI) and white matter fiber clustering method to uncover local white matter microstructures in PD with mild cognitive impairment (PD-MCI). This study included 23 PD-MCI and 20 PD with normal cognition (PD-NC) and 21 healthy controls (HC). To probe specific and fine-grained differences, metrics of NODDI and DTI in white matter fiber clusters were evaluated using along-tract analysis. Our results showed that PD-MCI patients had significantly lower neurite density index (NDI) and orientation dispersion index (ODI) in white matter fiber clusters in the prefrontal region. Correlation analysis and receiver operating characteristic (ROC) analysis revealed that the diagnostic performance of NODDI-derived metrics in cingulum bundle (2 clusters) and thalamo-frontal (2 clusters) were superior to DTI metrics. Our study provides a more specific insight to uncover local white matter abnormalities in PD-MCI, which benefit understanding the underlying mechanism of cognitive decline in PD and predicting the disease in advance.
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Affiliation(s)
- Chengzhe Zhang
- Institute of Information Processing and Automation, College of Information Engineering, Zhejiang University of Technology, Hangzhou, China
| | - Yuan Yuan
- Department of Neurology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Tian Sang
- Institute of Information Processing and Automation, College of Information Engineering, Zhejiang University of Technology, Hangzhou, China
| | - Lihua Yu
- Department of Neurology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yan Yu
- Institute of Information Processing and Automation, College of Information Engineering, Zhejiang University of Technology, Hangzhou, China
| | - Xiaoming Liu
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wenyang Zhou
- Institute of Information Processing and Automation, College of Information Engineering, Zhejiang University of Technology, Hangzhou, China
| | - Qingrun Zeng
- Institute of Information Processing and Automation, College of Information Engineering, Zhejiang University of Technology, Hangzhou, China
| | - Jingqiang Wang
- Institute of Information Processing and Automation, College of Information Engineering, Zhejiang University of Technology, Hangzhou, China
| | - Guoping Peng
- Department of Neurology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yuanjing Feng
- Institute of Information Processing and Automation, College of Information Engineering, Zhejiang University of Technology, Hangzhou, China
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19
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Xie L, Huang J, Yu J, Zeng Q, Hu Q, Chen Z, Xie G, Feng Y. CNTSeg: A multimodal deep-learning-based network for cranial nerves tract segmentation. Med Image Anal 2023; 86:102766. [PMID: 36812693 DOI: 10.1016/j.media.2023.102766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 09/21/2022] [Accepted: 02/08/2023] [Indexed: 02/12/2023]
Abstract
The segmentation of cranial nerves (CNs) tracts based on diffusion magnetic resonance imaging (dMRI) provides a valuable quantitative tool for the analysis of the morphology and course of individual CNs. Tractography-based approaches can describe and analyze the anatomical area of CNs by selecting the reference streamlines in combination with ROIs-based (regions-of-interests) or clustering-based. However, due to the slender structure of CNs and the complex anatomical environment, single-modality data based on dMRI cannot provide a complete and accurate description, resulting in low accuracy or even failure of current algorithms in performing individualized CNs segmentation. In this work, we propose a novel multimodal deep-learning-based multi-class network for automated cranial nerves tract segmentation without using tractography, ROI placement or clustering, called CNTSeg. Specifically, we introduced T1w images, fractional anisotropy (FA) images, and fiber orientation distribution function (fODF) peaks into the training data set, and design the back-end fusion module which uses the complementary information of the interphase feature fusion to improve the segmentation performance. CNTSeg has achieved the segmentation of 5 pairs of CNs (i.e. optic nerve CN II, oculomotor nerve CN III, trigeminal nerve CN V, and facial-vestibulocochlear nerve CN VII/VIII). Extensive comparisons and ablation experiments show promising results and are anatomically convincing even for difficult tracts. The code will be openly available at https://github.com/IPIS-XieLei/CNTSeg.
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Affiliation(s)
- Lei Xie
- Institute of Information Processing and Automation, College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China.
| | - Jiahao Huang
- Institute of Information Processing and Automation, College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China
| | - Jiangli Yu
- Institute of Information Processing and Automation, College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China
| | - Qingrun Zeng
- Institute of Information Processing and Automation, College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China
| | - Qiming Hu
- Institute of Information Processing and Automation, College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China
| | - Zan Chen
- Institute of Information Processing and Automation, College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China; Zhejiang Provincial United Key Laboratory of Embedded Systems, Hangzhou 310023, China
| | - Guoqiang Xie
- Nuclear Industry 215 Hospital of Shaanxi Province, Xianyang, 712000, China.
| | - Yuanjing Feng
- Institute of Information Processing and Automation, College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China; Zhejiang Provincial United Key Laboratory of Embedded Systems, Hangzhou 310023, China.
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A comparison of manual and automated neural architecture search for white matter tract segmentation. Sci Rep 2023; 13:1617. [PMID: 36709392 PMCID: PMC9884270 DOI: 10.1038/s41598-023-28210-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 01/16/2023] [Indexed: 01/30/2023] Open
Abstract
Segmentation of white matter tracts in diffusion magnetic resonance images is an important first step in many imaging studies of the brain in health and disease. Similar to medical image segmentation in general, a popular approach to white matter tract segmentation is to use U-Net based artificial neural network architectures. Despite many suggested improvements to the U-Net architecture in recent years, there is a lack of systematic comparison of architectural variants for white matter tract segmentation. In this paper, we evaluate multiple U-Net based architectures specifically for this purpose. We compare the results of these networks to those achieved by our own various architecture changes, as well as to new U-Net architectures designed automatically via neural architecture search (NAS). To the best of our knowledge, this is the first study to systematically compare multiple U-Net based architectures for white matter tract segmentation, and the first to use NAS. We find that the recently proposed medical imaging segmentation network UNet3+ slightly outperforms the current state of the art for white matter tract segmentation, and achieves a notably better mean Dice score for segmentation of the fornix (+ 0.01 and + 0.006 mean Dice increase for left and right fornix respectively), a tract that the current state of the art model struggles to segment. UNet3+ also outperforms the current state of the art when little training data is available. Additionally, manual architecture search found that a minor segmentation improvement is observed when an additional, deeper layer is added to the U-shape of UNet3+. However, all networks, including those designed via NAS, achieve similar results, suggesting that there may be benefit in exploring networks that deviate from the general U-Net paradigm.
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21
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Kender Z, Jende JME, Kurz FT, Tsilingiris D, Schimpfle L, Sulaj A, von Rauchhaupt E, Bartl H, Mooshage C, Göpfert J, Nawroth P, Herzig S, Szendroedi J, Bendszus M, Kopf S. Sciatic nerve fractional anisotropy and neurofilament light chain protein are related to sensorimotor deficit of the upper and lower limbs in patients with type 2 diabetes. Front Endocrinol (Lausanne) 2023; 14:1046690. [PMID: 37008917 PMCID: PMC10053786 DOI: 10.3389/fendo.2023.1046690] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 02/06/2023] [Indexed: 03/16/2023] Open
Abstract
BACKGROUND Diabetic sensorimotor polyneuropathy (DSPN) is one of the most prevalent and poorly understood diabetic microvascular complications. Recent studies have found that fractional anisotropy (FA), a marker for microstructural nerve integrity, is a sensitive parameter for the structural and functional nerve damage in DSPN. The aim of this study was to investigate the significance of proximal sciatic nerve's FA on different distal nerve fiber deficits of the upper and lower limbs and its correlation with the neuroaxonal biomarker, neurofilament light chain protein (NfL). MATERIALS AND METHODS Sixty-nine patients with type 2 diabetes (T2DM) and 30 healthy controls underwent detailed clinical and electrophysiological assessments, complete quantitative sensory testing (QST), and diffusion-weighted magnetic resonance neurography of the sciatic nerve. NfL was measured in the serum of healthy controls and patients with T2DM. Multivariate models were used to adjust for confounders of microvascular damage. RESULTS Patients with DSPN showed a 17% lower sciatic microstructural integrity compared to healthy controls (p<0.001). FA correlated with tibial and peroneal motor nerve conduction velocity (NCV) (r=0.6; p<0.001 and r=0.6; p<0.001) and sural sensory NCV (r=0.50; p<0.001). Participants with reduced sciatic nerve´s FA showed a loss of function of mechanical and thermal sensation of upper (r=0.3; p<0.01 and r=0.3; p<0.01) and lower (r=0.5; p<0.001 and r=0.3; p=<0.01) limbs and reduced functional performance of upper limbs (Purdue Pegboard Test for dominant hand; r=0.4; p<0.001). Increased levels of NfL and urinary albumin-creatinine ratio (ACR) were associated with loss of sciatic nerve´s FA (r=-0.5; p<0.001 and r= -0.3, p= 0.001). Of note, there was no correlation between sciatic FA and neuropathic symptoms or pain. CONCLUSION This is the first study showing that microstructural nerve integrity is associated with damage of different nerve fiber types and a neuroaxonal biomarker in DSPN. Furthermore, these findings show that proximal nerve damage is related to distal nerve function even before clinical symptoms occur. The microstructure of the proximal sciatic nerve and is also associated with functional nerve fiber deficits of the upper and lower limbs, suggesting that diabetic neuropathy involves structural changes of peripheral nerves of upper limbs too.
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Affiliation(s)
- Zoltan Kender
- Department of Endocrinology, Diabetology and Clinical Chemistry (Internal Medicine 1), Heidelberg University Hospital, Heidelberg, Germany
- German Center of Diabetes Research [Deutsches Zentrum für Diabetesforschung (DZD)], München, Germany
- *Correspondence: Zoltan Kender,
| | - Johann M. E. Jende
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Felix T. Kurz
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
- Department of Radiology, German Cancer Research Center, Heidelberg, Germany
| | - Dimitrios Tsilingiris
- Department of Endocrinology, Diabetology and Clinical Chemistry (Internal Medicine 1), Heidelberg University Hospital, Heidelberg, Germany
- German Center of Diabetes Research [Deutsches Zentrum für Diabetesforschung (DZD)], München, Germany
| | - Lukas Schimpfle
- Department of Endocrinology, Diabetology and Clinical Chemistry (Internal Medicine 1), Heidelberg University Hospital, Heidelberg, Germany
| | - Alba Sulaj
- Department of Endocrinology, Diabetology and Clinical Chemistry (Internal Medicine 1), Heidelberg University Hospital, Heidelberg, Germany
- German Center of Diabetes Research [Deutsches Zentrum für Diabetesforschung (DZD)], München, Germany
| | - Ekaterina von Rauchhaupt
- Department of Endocrinology, Diabetology and Clinical Chemistry (Internal Medicine 1), Heidelberg University Hospital, Heidelberg, Germany
- German Center of Diabetes Research [Deutsches Zentrum für Diabetesforschung (DZD)], München, Germany
| | - Hannelore Bartl
- Department of Endocrinology, Diabetology and Clinical Chemistry (Internal Medicine 1), Heidelberg University Hospital, Heidelberg, Germany
| | - Christoph Mooshage
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Jens Göpfert
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Peter Nawroth
- Department of Endocrinology, Diabetology and Clinical Chemistry (Internal Medicine 1), Heidelberg University Hospital, Heidelberg, Germany
- German Center of Diabetes Research [Deutsches Zentrum für Diabetesforschung (DZD)], München, Germany
- Joint-IDC Institute for Diabetes and Cancer, Heidelberg University, Heidelberg, Germany
| | - Stephan Herzig
- German Center of Diabetes Research [Deutsches Zentrum für Diabetesforschung (DZD)], München, Germany
- Joint-IDC Institute for Diabetes and Cancer, Heidelberg University, Heidelberg, Germany
- Joint-IDC Institute for Diabetes and Cancer, Helmholtz-Zentrum Munich, Munich, Germany
| | - Julia Szendroedi
- Department of Endocrinology, Diabetology and Clinical Chemistry (Internal Medicine 1), Heidelberg University Hospital, Heidelberg, Germany
- German Center of Diabetes Research [Deutsches Zentrum für Diabetesforschung (DZD)], München, Germany
- Joint-IDC Institute for Diabetes and Cancer, Heidelberg University, Heidelberg, Germany
| | - Martin Bendszus
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan Kopf
- Department of Endocrinology, Diabetology and Clinical Chemistry (Internal Medicine 1), Heidelberg University Hospital, Heidelberg, Germany
- German Center of Diabetes Research [Deutsches Zentrum für Diabetesforschung (DZD)], München, Germany
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22
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Yeh FC. Population-based tract-to-region connectome of the human brain and its hierarchical topology. Nat Commun 2022; 13:4933. [PMID: 35995773 PMCID: PMC9395399 DOI: 10.1038/s41467-022-32595-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 08/05/2022] [Indexed: 12/25/2022] Open
Abstract
Connectome maps region-to-region connectivities but does not inform which white matter pathways form the connections. Here we constructed a population-based tract-to-region connectome to fill this information gap. The constructed connectome quantifies the population probability of a white matter tract innervating a cortical region. The results show that ~85% of the tract-to-region connectome entries are consistent across individuals, whereas the remaining (~15%) have substantial individual differences requiring individualized mapping. Further hierarchical clustering on cortical regions revealed dorsal, ventral, and limbic networks based on the tract-to-region connective patterns. The clustering results on white matter bundles revealed the categorization of fiber bundle systems in the association pathways. This tract-to-region connectome provides insights into the connective topology between cortical regions and white matter bundles. The derived hierarchical relation further offers a categorization of gray and white matter structures. The brain connectome maps region-to-region connections but often ignores the role of the connecting pathways. Here, the authors mapped the tract-to-region relations to reveal the hierarchical relation of fiber bundles and dorsal, ventral, and limbic networks.
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Affiliation(s)
- Fang-Cheng Yeh
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, PA, USA. .,Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA.
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Zhang F, Daducci A, He Y, Schiavi S, Seguin C, Smith RE, Yeh CH, Zhao T, O'Donnell LJ. Quantitative mapping of the brain's structural connectivity using diffusion MRI tractography: A review. Neuroimage 2022; 249:118870. [PMID: 34979249 PMCID: PMC9257891 DOI: 10.1016/j.neuroimage.2021.118870] [Citation(s) in RCA: 78] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 12/03/2021] [Accepted: 12/31/2021] [Indexed: 12/13/2022] Open
Abstract
Diffusion magnetic resonance imaging (dMRI) tractography is an advanced imaging technique that enables in vivo reconstruction of the brain's white matter connections at macro scale. It provides an important tool for quantitative mapping of the brain's structural connectivity using measures of connectivity or tissue microstructure. Over the last two decades, the study of brain connectivity using dMRI tractography has played a prominent role in the neuroimaging research landscape. In this paper, we provide a high-level overview of how tractography is used to enable quantitative analysis of the brain's structural connectivity in health and disease. We focus on two types of quantitative analyses of tractography, including: 1) tract-specific analysis that refers to research that is typically hypothesis-driven and studies particular anatomical fiber tracts, and 2) connectome-based analysis that refers to research that is more data-driven and generally studies the structural connectivity of the entire brain. We first provide a review of methodology involved in three main processing steps that are common across most approaches for quantitative analysis of tractography, including methods for tractography correction, segmentation and quantification. For each step, we aim to describe methodological choices, their popularity, and potential pros and cons. We then review studies that have used quantitative tractography approaches to study the brain's white matter, focusing on applications in neurodevelopment, aging, neurological disorders, mental disorders, and neurosurgery. We conclude that, while there have been considerable advancements in methodological technologies and breadth of applications, there nevertheless remains no consensus about the "best" methodology in quantitative analysis of tractography, and researchers should remain cautious when interpreting results in research and clinical applications.
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Affiliation(s)
- Fan Zhang
- Brigham and Women's Hospital, Harvard Medical School, Boston, USA.
| | | | - Yong He
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China; Beijing Key Laboratory of Brain Imaging and Connectomics, Beijing Normal University, Beijing, China; IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China; Chinese Institute for Brain Research, Beijing, China
| | - Simona Schiavi
- Department of Computer Science, University of Verona, Verona, Italy
| | - Caio Seguin
- Melbourne Neuropsychiatry Centre, University of Melbourne and Melbourne Health, Melbourne, Australia; The University of Sydney, School of Biomedical Engineering, Sydney, Australia
| | - Robert E Smith
- The Florey Institute of Neuroscience and Mental Health, Melbourne, Australia; Florey Department of Neuroscience and Mental Health, The University of Melbourne, Melbourne, Australia
| | - Chun-Hung Yeh
- Institute for Radiological Research, Chang Gung University, Taoyuan, Taiwan; Department of Psychiatry, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Tengda Zhao
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China; Beijing Key Laboratory of Brain Imaging and Connectomics, Beijing Normal University, Beijing, China; IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China
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24
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Kai J, Khan AR. Assessing the Reliability of Template-Based Clustering for Tractography in Healthy Human Adults. Front Neuroinform 2022; 16:777853. [PMID: 35250526 PMCID: PMC8891507 DOI: 10.3389/fninf.2022.777853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 01/06/2022] [Indexed: 11/21/2022] Open
Abstract
Tractography is a non-invasive technique to investigate the brain’s structural pathways (also referred to as tracts) that connect different brain regions. 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. However, the reliability of this approach has not been extensively studied. Here, an investigation into template-based clustering reliability was performed, assessing the output from two datasets: Human Connectome Project (HCP) and MyConnectome project. The effect of intersubject variability on template-based clustering reliability was investigated, as well as the reliability of both deep and superficial white matter tracts. Identified tracts were evaluated by assessing Euclidean distances from a dataset-specific tract average centroid, the volumetric overlap across corresponding tracts, and along-tract agreement of quantitative values. Further, two template-based techniques were employed to evaluate the reliability of different clustering approaches. Reliability assessment can increase the confidence of a tract identifying technique in future applications to study pathways of interest. The two different template-based approaches exhibited similar reliability for identifying both deep white matter tracts and the superficial white matter.
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Affiliation(s)
- Jason Kai
- Department of Medical Biophysics, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON, Canada
- Centre for Functional and Metabolic Mapping, Robarts Research Institute, The University of Western Ontario, London, ON, Canada
| | - Ali R. Khan
- Department of Medical Biophysics, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON, Canada
- Centre for Functional and Metabolic Mapping, Robarts Research Institute, The University of Western Ontario, London, ON, Canada
- *Correspondence: Ali R. Khan,
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25
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Huang J, Li M, Zeng Q, Xie L, He J, Chen G, Liang J, Li M, Feng Y. Automatic oculomotor nerve identification based on
data‐driven
fiber clustering. Hum Brain Mapp 2022; 43:2164-2180. [PMID: 35092135 PMCID: PMC8996358 DOI: 10.1002/hbm.25779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 12/09/2021] [Accepted: 12/26/2021] [Indexed: 11/10/2022] Open
Abstract
The oculomotor nerve (OCN) is the main motor nerve innervating eye muscles and can be involved in multiple flammatory, compressive, or pathologies. The diffusion magnetic resonance imaging (dMRI) tractography is now widely used to describe the trajectory of the OCN. However, the complex cranial structure leads to difficulties in fiber orientation distribution (FOD) modeling, fiber tracking, and region of interest (ROI) selection. Currently, the identification of OCN relies on expert manual operation, resulting in challenges, such as the carries high clinical, time‐consuming, and labor costs. Thus, we propose a method that can automatically identify OCN from dMRI tractography. First, we choose the multi‐shell multi‐tissue constraint spherical deconvolution (MSMT‐CSD) FOD estimation model and deterministic tractography to describe the 3D trajectory of the OCN. Then, we rely on the well‐established computational pipeline and anatomical expertise to create a data‐driven OCN tractography atlas from 40 HCP data. We identify six clusters belonging to the OCN from the atlas, including the structures of three kinds of positional relationships (pass between, pass through, and go around) with the red nuclei and two kinds of positional relationships with medial longitudinal fasciculus. Finally, we apply the proposed OCN atlas to identify the OCN automatically from 40 new HCP subjects and two patients with brainstem cavernous malformation. In terms of spatial overlap and visualization, experiment results show that the automatically and manually identified OCN fibers are consistent. Our proposed OCN atlas provides an effective tool for identifying OCN by avoiding the traditional selection strategy of ROIs.
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Affiliation(s)
- Jiahao Huang
- Institute of Information Processing and Automation, College of Information Engineering, Zhejiang University of Technology Hangzhou China
- Zhejiang Provincial United Key Laboratory of Embedded Systems Hangzhou China
| | - Mengjun Li
- Department of Radiology, Second Xiangya Hospital Central South University Hunan China
- Department of Neurosurgery Capital Medical University Xuanwu Hospital Beijing China
| | - Qingrun Zeng
- Institute of Information Processing and Automation, College of Information Engineering, Zhejiang University of Technology Hangzhou China
- Zhejiang Provincial United Key Laboratory of Embedded Systems Hangzhou China
| | - Lei Xie
- Institute of Information Processing and Automation, College of Information Engineering, Zhejiang University of Technology Hangzhou China
- Zhejiang Provincial United Key Laboratory of Embedded Systems Hangzhou China
| | - Jianzhong He
- Institute of Information Processing and Automation, College of Information Engineering, Zhejiang University of Technology Hangzhou China
- Zhejiang Provincial United Key Laboratory of Embedded Systems Hangzhou China
| | - Ge Chen
- Department of Neurosurgery Capital Medical University Xuanwu Hospital Beijing China
| | - Jiantao Liang
- Department of Neurosurgery Capital Medical University Xuanwu Hospital Beijing China
| | - Mingchu Li
- Department of Neurosurgery Capital Medical University Xuanwu Hospital Beijing China
| | - Yuanjing Feng
- Institute of Information Processing and Automation, College of Information Engineering, Zhejiang University of Technology Hangzhou China
- Zhejiang Provincial United Key Laboratory of Embedded Systems Hangzhou China
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26
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Jende JME, Kender Z, Morgenstern J, Renn P, Mooshage C, Juerchott A, Kopf S, Nawroth PP, Bendszus M, Kurz FT. Fractional Anisotropy and Troponin T Parallel Structural Nerve Damage at the Upper Extremities in a Group of Patients With Prediabetes and Type 2 Diabetes – A Study Using 3T Magnetic Resonance Neurography. Front Neurosci 2022; 15:741494. [PMID: 35140582 PMCID: PMC8818845 DOI: 10.3389/fnins.2021.741494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 12/17/2021] [Indexed: 12/14/2022] Open
Abstract
Background Recent studies have found that troponin T parallels the structural and functional decay of peripheral nerves at the level of the lower limbs in patients with type 2 diabetes (T2D). The aim of this study was to determine whether this finding can also be reproduced at the level of the upper limbs. Methods Ten patients with fasting glucose levels >100 mg/dl (five with prediabetes and five with T2D) underwent magnetic resonance neurography of the right upper arm comprising T2-weighted and diffusion weighted sequences. The fractional anisotropy (FA), an indicator for the structural integrity of peripheral nerves, was calculated in an automated approach for the median, ulnar, and radial nerve. All participants underwent additional clinical, serological, and electrophysiological assessments. Results High sensitivity Troponin T (hsTNT) and HbA1c were negatively correlated with the average FA of the median, ulnar and radial nerve (r = −0.84; p = 0.002 and r = −0.68; p = 0.032). Both FA and hsTNT further showed correlations with items of the Michigan Hand Outcome Questionnaire (r = −0.76; p = 0.010 and r = 0.87; p = 0.001, respectively). A negative correlation was found for hsTNT and HbA1c with the total Purdue Pegboard Test Score (r = −0.87; p = 0.001 and r = −0.68; p = 0.031). Conclusion This study is the first to find that hsTNT and HbA1c are associated with functional and structural parameters of the nerves at the level of the upper limbs in patients with impaired glucose tolerance and T2D. Our results support the hypothesis that hyperglycemia-related microangiopathy, represented by elevated hsTNT levels, is a contributor to nerve damage in diabetic polyneuropathy.
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Affiliation(s)
- Johann M. E. Jende
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Zoltan Kender
- Department of Endocrinology, Diabetology and Clinical Chemistry, Heidelberg University Hospital, Heidelberg, Germany
| | - Jakob Morgenstern
- Department of Endocrinology, Diabetology and Clinical Chemistry, Heidelberg University Hospital, Heidelberg, Germany
| | - Pascal Renn
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Alexander Juerchott
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan Kopf
- Department of Endocrinology, Diabetology and Clinical Chemistry, Heidelberg University Hospital, Heidelberg, Germany
- German Center of Diabetes Research, München, Germany
| | - Peter P. Nawroth
- Department of Endocrinology, Diabetology and Clinical Chemistry, Heidelberg University Hospital, Heidelberg, Germany
- German Center of Diabetes Research, München, Germany
- Joint Institute for Diabetes and Cancer at Helmholtz-Zentrum Munich and Heidelberg University, Heidelberg, Germany
| | - Martin Bendszus
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Felix T. Kurz
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Research Center, Radiology E010, Heidelberg, Germany
- *Correspondence: Felix T. Kurz,
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27
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Big Data in Cognitive Neuroscience: Opportunities and Challenges. BIG DATA ANALYTICS 2022. [DOI: 10.1007/978-3-031-24094-2_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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28
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Li M, Yeh FC, Zeng Q, Wu X, Wang X, Zhu Z, Liu X, Liang J, Chen G, Zhang H, Feng Y, Li M. The trajectory of the medial longitudinal fasciculus in the human brain: A diffusion imaging-based tractography study. Hum Brain Mapp 2021; 42:6070-6086. [PMID: 34597450 PMCID: PMC8596984 DOI: 10.1002/hbm.25670] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 09/04/2021] [Accepted: 09/10/2021] [Indexed: 01/23/2023] Open
Abstract
The aim of this study is to investigate the trajectory of medial longitudinal fasciculus (MLF) and explore its anatomical relationship with the oculomotor nerve using tractography technique. The MLF and oculomotor nerve were reconstructed at the same time with preset three region of interests (ROIs): one set at the area of rostral midbrain, one placed on the MLF area at the upper pons, and one placed at the cisternal part of the oculomotor nerve. This mapping protocol was tested in an HCP‐1065 template, 35 health subjects from Massachusetts General Hospital (MGH), 20 healthy adults and 6 brainstem cavernous malformation (BCM) patients with generalized q‐sampling imaging (GQI)‐based tractography. Finally, the 200 μm brainstem template from Center for In Vivo Microscopy, Duke University (Duke CIVM), was used to validate the trajectory of reconstructed MLF. The MLF and oculomotor nerve were reconstructed in the HCP‐1065 template, 35 MGH health subjects, 20 healthy adults and 6 BCM patients. The MLF was in conjunction with the ipsilateral mesencephalic part of the oculomotor nerve. The displacement of MLF was identified in all BCM patients. Decreased QA, RDI and FA were found in the MLF of lesion side, indicating axonal loss and/or edema of displaced MLF. The reconstructed MLF in Duke CIVM brainstem 200 μm template corresponded well with histological anatomy. The MLF and oculomotor nerve were visualized accurately with our protocol using GQI‐based fiber tracking. This GQI‐based tractography is an important tool in the reconstruction and evaluation of MLF.
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Affiliation(s)
- Mengjun Li
- Department of Neurosurgery, Capital Medical University Xuanwu Hospital, Beijing, China
| | - Fang-Cheng Yeh
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,Department of Bioengineering, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Qingrun Zeng
- Institute of Information Processing and Automation, College of Information Engineering, Zhejiang University of Technology, Hangzhou, China.,Zhejiang Provincial United Key Laboratory of Embedded Systems, Hangzhou, China
| | - Xiaolong Wu
- Department of Neurosurgery, Capital Medical University Xuanwu Hospital, Beijing, China
| | - Xu Wang
- Department of Neurosurgery, Capital Medical University Xuanwu Hospital, Beijing, China
| | - Zixin Zhu
- Department of Neurosurgery, Capital Medical University Xuanwu Hospital, Beijing, China
| | - Xiaohai Liu
- Department of Neurosurgery, Capital Medical University Xuanwu Hospital, Beijing, China
| | - Jiantao Liang
- Department of Neurosurgery, Capital Medical University Xuanwu Hospital, Beijing, China
| | - Ge Chen
- Department of Neurosurgery, Capital Medical University Xuanwu Hospital, Beijing, China
| | - Hongqi Zhang
- Department of Neurosurgery, Capital Medical University Xuanwu Hospital, Beijing, China
| | - Yuanjing Feng
- Institute of Information Processing and Automation, College of Information Engineering, Zhejiang University of Technology, Hangzhou, China.,Zhejiang Provincial United Key Laboratory of Embedded Systems, Hangzhou, China
| | - Mingchu Li
- Department of Neurosurgery, Capital Medical University Xuanwu Hospital, Beijing, China
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29
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Yeh FC, Irimia A, Bastos DCDA, Golby AJ. Tractography methods and findings in brain tumors and traumatic brain injury. Neuroimage 2021; 245:118651. [PMID: 34673247 PMCID: PMC8859988 DOI: 10.1016/j.neuroimage.2021.118651] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 10/05/2021] [Accepted: 10/11/2021] [Indexed: 12/31/2022] Open
Abstract
White matter fiber tracking using diffusion magnetic resonance imaging (dMRI) provides a noninvasive approach to map brain connections, but improving anatomical accuracy has been a significant challenge since the birth of tractography methods. Utilizing tractography in brain studies therefore requires understanding of its technical limitations to avoid shortcomings and pitfalls. This review explores tractography limitations and how different white matter pathways pose different challenges to fiber tracking methodologies. We summarize the pros and cons of commonly-used methods, aiming to inform how tractography and its related analysis may lead to questionable results. Extending these experiences, we review the clinical utilization of tractography in patients with brain tumors and traumatic brain injury, starting from tensor-based tractography to more advanced methods. We discuss current limitations and highlight novel approaches in the context of these two conditions to inform future tractography developments.
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Affiliation(s)
- Fang-Cheng Yeh
- Department of Neurological Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA; Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
| | - Andrei Irimia
- Ethel Percy Andrus Gerontology Center, Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, USA; Corwin D. Denney Research Center, Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, California, USA
| | | | - Alexandra J Golby
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA; Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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30
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Zeng Q, Li M, Yuan S, He J, Wang J, Chen Z, Zhao C, Chen G, Liang J, Li M, Feng Y. Automated facial-vestibulocochlear nerve complex identification based on data-driven tractography clustering. NMR IN BIOMEDICINE 2021; 34:e4607. [PMID: 34486766 DOI: 10.1002/nbm.4607] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 08/04/2021] [Accepted: 08/07/2021] [Indexed: 06/13/2023]
Abstract
Small size and intricate anatomical environment are the main difficulties facing tractography of the facial-vestibulocochlear nerve complex (FVN), and lead to challenges in fiber orientation distribution (FOD) modeling, fiber tracking, region-of-interest selection, and fiber filtering. Experts need rich experience in anatomy and tractography, as well as substantial labor costs, to identify the FVN. Thus, we present a pipeline to identify the FVN automatically, in what we believe is the first study of the automated identification of the FVN. First, we created an FVN template. Forty high-resolution multishell data were used to perform data-driven fiber clustering based on the multishell multitissue constraint spherical deconvolution FOD model and deterministic tractography. We selected the brainstem and cerebellum (BS-CB) region as the seed region and removed the fibers that reach other brain regions. We then performed spectral fiber clustering twice. The first clustering was to create a BS-CB atlas and separate the fibers that pass through the cerebellopontine angle, and the other one was to extract the FVN. Second, we registered the subject-specific fibers in the space of the FVN template and assigned each fiber to the closest cluster to identify the FVN automatically by spectral embedding. We applied the proposed method to different acquirement sites, including two different healthy datasets and two tumor patient datasets. Experimental results showed that our automatic identification results have ideal colocalization with expert manual identification in terms of spatial overlap and visualization. Importantly, we successfully applied our method to tumor patient data. The FVNs identified by the proposed method were in agreement with intraoperative findings.
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Affiliation(s)
- Qingrun Zeng
- Institute of Information Processing and Automation, College of Information Engineering, Zhejiang University of Technology, Hangzhou, China
- Zhejiang Provincial United Key Laboratory of Embedded Systems, Hangzhou, China
| | - Mengjun Li
- Department of Radiology, Second Xiangya Hospital, Central South University, Changsha, China
- Department of Neurosurgery, Capital Medical University Xuanwu Hospital, Beijing, China
| | - Shaonan Yuan
- Institute of Information Processing and Automation, College of Information Engineering, Zhejiang University of Technology, Hangzhou, China
- Zhejiang Provincial United Key Laboratory of Embedded Systems, Hangzhou, China
| | - Jianzhong He
- Institute of Information Processing and Automation, College of Information Engineering, Zhejiang University of Technology, Hangzhou, China
- Zhejiang Provincial United Key Laboratory of Embedded Systems, Hangzhou, China
| | - Jingqiang Wang
- Institute of Information Processing and Automation, College of Information Engineering, Zhejiang University of Technology, Hangzhou, China
- Zhejiang Provincial United Key Laboratory of Embedded Systems, Hangzhou, China
| | - Zan Chen
- Institute of Information Processing and Automation, College of Information Engineering, Zhejiang University of Technology, Hangzhou, China
- Zhejiang Provincial United Key Laboratory of Embedded Systems, Hangzhou, China
| | - Changchen Zhao
- Institute of Information Processing and Automation, College of Information Engineering, Zhejiang University of Technology, Hangzhou, China
- Zhejiang Provincial United Key Laboratory of Embedded Systems, Hangzhou, China
| | - Ge Chen
- Department of Neurosurgery, Capital Medical University Xuanwu Hospital, Beijing, China
| | - Jiantao Liang
- Department of Neurosurgery, Capital Medical University Xuanwu Hospital, Beijing, China
| | - Mingchu Li
- Department of Neurosurgery, Capital Medical University Xuanwu Hospital, Beijing, China
| | - Yuanjing Feng
- Institute of Information Processing and Automation, College of Information Engineering, Zhejiang University of Technology, Hangzhou, China
- Zhejiang Provincial United Key Laboratory of Embedded Systems, Hangzhou, China
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Wu C, Ferreira F, Fox M, Harel N, Hattangadi-Gluth J, Horn A, Jbabdi S, Kahan J, Oswal A, Sheth SA, Tie Y, Vakharia V, Zrinzo L, Akram H. Clinical applications of magnetic resonance imaging based functional and structural connectivity. Neuroimage 2021; 244:118649. [PMID: 34648960 DOI: 10.1016/j.neuroimage.2021.118649] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 09/24/2021] [Accepted: 10/10/2021] [Indexed: 12/23/2022] Open
Abstract
Advances in computational neuroimaging techniques have expanded the armamentarium of imaging tools available for clinical applications in clinical neuroscience. Non-invasive, in vivo brain MRI structural and functional network mapping has been used to identify therapeutic targets, define eloquent brain regions to preserve, and gain insight into pathological processes and treatments as well as prognostic biomarkers. These tools have the real potential to inform patient-specific treatment strategies. Nevertheless, a realistic appraisal of clinical utility is needed that balances the growing excitement and interest in the field with important limitations associated with these techniques. Quality of the raw data, minutiae of the processing methodology, and the statistical models applied can all impact on the results and their interpretation. A lack of standardization in data acquisition and processing has also resulted in issues with reproducibility. This limitation has had a direct impact on the reliability of these tools and ultimately, confidence in their clinical use. Advances in MRI technology and computational power as well as automation and standardization of processing methods, including machine learning approaches, may help address some of these issues and make these tools more reliable in clinical use. In this review, we will highlight the current clinical uses of MRI connectomics in the diagnosis and treatment of neurological disorders; balancing emerging applications and technologies with limitations of connectivity analytic approaches to present an encompassing and appropriate perspective.
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Affiliation(s)
- Chengyuan Wu
- Department of Neurological Surgery, Vickie and Jack Farber Institute for Neuroscience, Thomas Jefferson University, 909 Walnut Street, Third Floor, Philadelphia, PA 19107, USA; Jefferson Integrated Magnetic Resonance Imaging Center, Department of Radiology, Thomas Jefferson University, 909 Walnut Street, First Floor, Philadelphia, PA 19107, USA.
| | - Francisca Ferreira
- Victor Horsley Department of Neurosurgery, National Hospital for Neurology and Neurosurgery, 33 Queen Square, London WC1N 3BG, UK; Unit of Functional Neurosurgery, UCL Queen Square Institute of Neurology, 33 Queen Square, London WC1N 3BG, UK.
| | - Michael Fox
- Center for Brain Circuit Therapeutics, Departments of Neurology, Psychiatry, Radiology, and Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, 60 Fenwood Road, Boston, MA 02115, USA.
| | - Noam Harel
- Center for Magnetic Resonance Research, University of Minnesota, 2021 Sixth Street S.E., Minneapolis, MN 55455, USA.
| | - Jona Hattangadi-Gluth
- Department of Radiation Medicine and Applied Sciences, Center for Precision Radiation Medicine, University of California, San Diego, 3855 Health Sciences Drive, La Jolla, CA 92037, USA.
| | - Andreas Horn
- Neurology Department, Movement Disorders and Neuromodulation Section, Charité - University Medicine Berlin, Charitéplatz 1, D-10117, Berlin, Germany.
| | - Saad Jbabdi
- Wellcome Centre for Integrative Neuroimaging, Centre for Functional MRI of the Brain, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK.
| | - Joshua Kahan
- Department of Neurology, Weill Cornell Medicine, 525 East 68th Street, New York, NY, 10065, USA.
| | - Ashwini Oswal
- Medical Research Council Brain Network Dynamics Unit, University of Oxford, Mansfield Rd, Oxford OX1 3TH, UK.
| | - Sameer A Sheth
- Department of Neurosurgery, Baylor College of Medicine, 7200 Cambridge, Ninth Floor, Houston, TX 77030, USA.
| | - Yanmei Tie
- Center for Brain Circuit Therapeutics, Departments of Neurology, Psychiatry, Radiology, and Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, 60 Fenwood Road, Boston, MA 02115, USA; Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, 60 Fenwood Road, Boston, MA 02115, USA.
| | - Vejay Vakharia
- Victor Horsley Department of Neurosurgery, National Hospital for Neurology and Neurosurgery, 33 Queen Square, London WC1N 3BG, UK.
| | - Ludvic Zrinzo
- Victor Horsley Department of Neurosurgery, National Hospital for Neurology and Neurosurgery, 33 Queen Square, London WC1N 3BG, UK; Unit of Functional Neurosurgery, UCL Queen Square Institute of Neurology, 33 Queen Square, London WC1N 3BG, UK.
| | - Harith Akram
- Victor Horsley Department of Neurosurgery, National Hospital for Neurology and Neurosurgery, 33 Queen Square, London WC1N 3BG, UK; Unit of Functional Neurosurgery, UCL Queen Square Institute of Neurology, 33 Queen Square, London WC1N 3BG, UK.
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32
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Richards TJ, Anderson KL, Anderson JS. "Fully automated segmentation of the corticospinal tract using the TractSeg algorithm in patients with brain tumors". Clin Neurol Neurosurg 2021; 210:107001. [PMID: 34749021 DOI: 10.1016/j.clineuro.2021.107001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 11/18/2022]
Abstract
OBJECTIVE Tractography has been used to define the presurgical location of white matter tracts, but this is subjective and time-intensive, making incorporation to imaging workflow at scale problematic. The objective is to validate a fully automated pipeline using the TractSeg algorithm (Wasserthal et al. NeuroImage 2018;183:239-253) to segment the corticospinal tract in patients with brain tumors adjacent to the corticospinal tract. METHODS The process of importing a structural MPRAGE sequence and raw diffusion weighted images from PACS, executing the TractSeg algorithm, overlaying the resulting bilateral corticospinal tracts on the MPRAGE image, and exporting this composite image to PACS was automated. This procedure was used to segment the corticospinal tract in 28 patients with brain masses adjacent to or displacing the corticospinal tract. These segmentations were compared with both manual deterministic tractography performed with DSI Studio using seeds placed in the pons and an automated tractography method in DSI Studio. RESULTS The automated algorithm was able to segment the bilateral corticospinal tracts in all 28 patients whereas the manual reference method and DSI Studio based automated tractography were unsuccessful in 2 and 1 patients, respectively. In all cases, the TractSeg segmentations very closely matched the manual segmentations. Also, TractSeg appeared to include larger portions of the lateral corticospinal tract fibers than the other 2 methods. CONCLUSION The TractSeg algorithm demonstrated robust performance in segmenting the corticospinal tract in patients with brain tumors adjacent to this tract. The algorithm is fast to perform and has great potential for optimizing and streamlining neurosurgical planning.
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Affiliation(s)
- Tyler J Richards
- University of Utah School of Medicine, Department of Radiology and Imaging Sciences, 30 North 1900 East #1A071, Salt Lake City, UT 84132-2140, USA.
| | - Keri L Anderson
- University of Utah School of Computing, Department of Computer Science, Merrill Engineering, 50 Central Campus Dr, Salt Lake City, UT 84112, USA.
| | - Jeffrey S Anderson
- University of Utah School of Medicine, Department of Radiology and Imaging Sciences, 30 North 1900 East #1A071, Salt Lake City, UT 84132-2140, USA.
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Levitt JJ, Zhang F, Vangel M, Nestor PG, Rathi Y, Kubicki M, Shenton ME, O'Donnell LJ. The Organization of Frontostriatal Brain Wiring in Healthy Subjects Using a Novel Diffusion Imaging Fiber Cluster Analysis. Cereb Cortex 2021; 31:5308-5318. [PMID: 34180506 DOI: 10.1093/cercor/bhab159] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 11/14/2022] Open
Abstract
To assess normal organization of frontostriatal brain wiring, we analyzed diffusion magnetic resonance imaging (dMRI) scans in 100 young adult healthy subjects (HSs). We identified fiber clusters intersecting the frontal cortex and caudate, a core component of associative striatum, and quantified their degree of deviation from a strictly topographic pattern. Using whole brain dMRI tractography and an automated tract parcellation clustering method, we extracted 17 white matter fiber clusters per hemisphere connecting the frontal cortex and caudate. In a novel approach to quantify the geometric relationship among clusters, we measured intercluster endpoint distances between corresponding cluster pairs in the frontal cortex and caudate. We show first, the overall frontal cortex wiring pattern of the caudate deviates from a strictly topographic organization due to significantly greater convergence in regionally specific clusters; second, these significantly convergent clusters originate in subregions of ventrolateral, dorsolateral, and orbitofrontal prefrontal cortex (PFC); and, third, a similar organization in both hemispheres. Using a novel tractography method, we find PFC-caudate brain wiring in HSs deviates from a strictly topographic organization due to a regionally specific pattern of cluster convergence. We conjecture cortical subregions projecting to the caudate with greater convergence subserve functions that benefit from greater circuit integration.
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Affiliation(s)
- J J Levitt
- Department of Psychiatry, VA Boston Healthcare System, Brockton Division, Brockton MA 02301, USA.,Department of Psychiatry, Harvard Medical School, Boston, MA 02115, USA.,Department of Psychiatry, Psychiatry Neuroimaging Laboratory, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - F Zhang
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - M Vangel
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - P G Nestor
- Department of Psychiatry, VA Boston Healthcare System, Brockton Division, Brockton MA 02301, USA.,Department of Psychiatry, Harvard Medical School, Boston, MA 02115, USA.,Department of Psychology, University of Massachusetts, Boston, MA 02125, USA
| | - Y Rathi
- Department of Psychiatry, Psychiatry Neuroimaging Laboratory, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA.,Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - M Kubicki
- Department of Psychiatry, Psychiatry Neuroimaging Laboratory, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA.,Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - M E Shenton
- Department of Psychiatry, Psychiatry Neuroimaging Laboratory, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA.,Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - L J O'Donnell
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
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Goicovich I, Olivares P, Román C, Vázquez A, Poupon C, Mangin JF, Guevara P, Hernández C. Fiber Clustering Acceleration With a Modified Kmeans++ Algorithm Using Data Parallelism. Front Neuroinform 2021; 15:727859. [PMID: 34539370 PMCID: PMC8445177 DOI: 10.3389/fninf.2021.727859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 08/10/2021] [Indexed: 11/13/2022] Open
Abstract
Fiber clustering methods are typically used in brain research to study the organization of white matter bundles from large diffusion MRI tractography datasets. These methods enable exploratory bundle inspection using visualization and other methods that require identifying brain white matter structures in individuals or a population. Some applications, such as real-time visualization and inter-subject clustering, need fast and high-quality intra-subject clustering algorithms. This work proposes a parallel algorithm using a General Purpose Graphics Processing Unit (GPGPU) for fiber clustering based on the FFClust algorithm. The proposed GPGPU implementation exploits data parallelism using both multicore and GPU fine-grained parallelism present in commodity architectures, including current laptops and desktop computers. Our approach implements all FFClust steps in parallel, improving execution times in all of them. In addition, our parallel approach includes a parallel Kmeans++ algorithm implementation and defines a new variant of Kmeans++ to reduce the impact of choosing outliers as initial centroids. The results show that our approach provides clustering quality results very similar to FFClust, and it requires an execution time of 3.5 s for processing about a million fibers, achieving a speedup of 11.5 times compared to FFClust.
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Affiliation(s)
- Isaac Goicovich
- Department of Electrical Engineering, Universidad de Concepción, Concepción, Chile
| | - Paulo Olivares
- Department of Computer Science, Universidad de Concepción, Concepción, Chile
| | - Claudio Román
- Department of Electrical Engineering, Universidad de Concepción, Concepción, Chile
| | - Andrea Vázquez
- Department of Computer Science, Universidad de Concepción, Concepción, Chile
| | - Cyril Poupon
- Université Paris-Saclay, CEA, CNRS, Neurospin, Baobab, Gif-sur-Yvette, France
| | | | - Pamela Guevara
- Department of Electrical Engineering, Universidad de Concepción, Concepción, Chile
| | - Cecilia Hernández
- Department of Computer Science, Universidad de Concepción, Concepción, Chile.,Center for Biotechnology and Bioengineering, Santiago, Chile
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Li M, Ribas EC, Zhang Z, Wu X, Wang X, Liu X, Liang J, Chen G, Li M. Tractography of the ansa lenticularis in the human brain. Clin Anat 2021; 35:269-279. [PMID: 34535922 DOI: 10.1002/ca.23788] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/02/2021] [Accepted: 09/08/2021] [Indexed: 12/31/2022]
Abstract
The aim of this study was to make a thorough investigation of the trajectory of the ansa lenticularis (AL) and its subcomponents using high-resolution fiber-tracking tractography. The subcomponents of the AL were reconstructed from one region of interest (ROI) in the area of the globus pallidus combined with another ROI in the red nucleus, substantia nigra, subthalamic nucleus, or thalamus. This fiber-tracking protocol was tested in an HCP-1065 template, 35 healthy subjects from Massachusetts General Hospital (MGH), and 20 healthy subjects from the human connectome project (HCP) using generalized q-sampling imaging (GQI)-based tractography. Quantitative anisotropy and fractional anisotropy were also computed for the AL subcomponents. The subcomponents of the AL could be reconstructed in the HCP-1065 template, 35 MGH healthy subjects, and 20 HCP healthy subjects. The AL descends from the globus pallidus and joins the ansa peduncularis for a short distance, subdividing later into fibers that continue separately to the red nucleus, substantia nigra, subthalamic nucleus, and thalamus. The study demonstrated the trajectory of the ansa lenticularis and its subcomponents using GQI-based tractography, improving our understanding of the anatomical connectivity between the globus pallidus and the thalamo-subthalamic region in the human brain. One Sentence Summary The investigation of the ansa lenticularis and its subcomponents using high-resolution diffusion images based tractography.
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Affiliation(s)
- Mengjun Li
- Department of Neurosurgery, Samii Clinical Neuroanatomy Research & Education Center, Capital Medical University Xuanwu Hospital, China International Neuroscience Institute (China-INI), Beijing, China
| | - Eduardo Carvalhal Ribas
- Division of Neurosurgery, Hospital das Clínicas, University of São Paulo Medical School, São Paulo, Brazil
| | - Zhiping Zhang
- Department of Neurosurgery, Samii Clinical Neuroanatomy Research & Education Center, Capital Medical University Xuanwu Hospital, China International Neuroscience Institute (China-INI), Beijing, China
| | - Xiaolong Wu
- Department of Neurosurgery, Samii Clinical Neuroanatomy Research & Education Center, Capital Medical University Xuanwu Hospital, China International Neuroscience Institute (China-INI), Beijing, China
| | - Xu Wang
- Department of Neurosurgery, Samii Clinical Neuroanatomy Research & Education Center, Capital Medical University Xuanwu Hospital, China International Neuroscience Institute (China-INI), Beijing, China
| | - Xiaohai Liu
- Department of Neurosurgery, Samii Clinical Neuroanatomy Research & Education Center, Capital Medical University Xuanwu Hospital, China International Neuroscience Institute (China-INI), Beijing, China
| | - Jiantao Liang
- Department of Neurosurgery, Samii Clinical Neuroanatomy Research & Education Center, Capital Medical University Xuanwu Hospital, China International Neuroscience Institute (China-INI), Beijing, China
| | - Ge Chen
- Department of Neurosurgery, Samii Clinical Neuroanatomy Research & Education Center, Capital Medical University Xuanwu Hospital, China International Neuroscience Institute (China-INI), Beijing, China
| | - Mingchu Li
- Department of Neurosurgery, Samii Clinical Neuroanatomy Research & Education Center, Capital Medical University Xuanwu Hospital, China International Neuroscience Institute (China-INI), Beijing, China
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Wu Y, Ahmad S, Yap PT. Highly Reproducible Whole Brain Parcellation in Individuals via Voxel Annotation with Fiber Clusters. MEDICAL IMAGE COMPUTING AND COMPUTER-ASSISTED INTERVENTION : MICCAI ... INTERNATIONAL CONFERENCE ON MEDICAL IMAGE COMPUTING AND COMPUTER-ASSISTED INTERVENTION 2021; 12907:477-486. [PMID: 36200667 PMCID: PMC9531918 DOI: 10.1007/978-3-030-87234-2_45] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
A central goal in systems neuroscience is to parcellate the brain into discrete units that are neurobiologically coherent. Here, we propose a strategy for consistent whole-brain parcellation of white matter (WM) and gray matter (GM) in individuals. We parcellate the brain into coherent parcels using non-negative matrix factorization based on voxel annotation using fiber clusters. Tractography is performed using an algorithm that mitigates gyral bias, allowing full gyral and sulcal coverage for reliable parcellation of the cortical ribbon. Experimental results indicate that parcellation using our approach is highly reproducible with 100% test-retest parcel identification rate and is highly consistent with significantly lower inter-subject variability than FreeSurfer parcellation. This implies that reproducible parcellation can be obtained for subject-specific investigation of brain structure and function.
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Affiliation(s)
- Ye Wu
- Department of Radiology and Biomedical Research Imaging Center (BRIC), The University of North Carolina at Chapel Hill, NC, USA
| | - Sahar Ahmad
- Department of Radiology and Biomedical Research Imaging Center (BRIC), The University of North Carolina at Chapel Hill, NC, USA
| | - Pew-Thian Yap
- Department of Radiology and Biomedical Research Imaging Center (BRIC), The University of North Carolina at Chapel Hill, NC, USA
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Yang JYM, Yeh CH, Poupon C, Calamante F. Diffusion MRI tractography for neurosurgery: the basics, current state, technical reliability and challenges. Phys Med Biol 2021; 66. [PMID: 34157706 DOI: 10.1088/1361-6560/ac0d90] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 06/22/2021] [Indexed: 01/20/2023]
Abstract
Diffusion magnetic resonance imaging (dMRI) tractography is currently the only imaging technique that allows for non-invasive delineation and visualisation of white matter (WM) tractsin vivo,prompting rapid advances in related fields of brain MRI research in recent years. One of its major clinical applications is for pre-surgical planning and intraoperative image guidance in neurosurgery, where knowledge about the location of WM tracts nearby the surgical target can be helpful to guide surgical resection and optimise post-surgical outcomes. Surgical injuries to these WM tracts can lead to permanent neurological and functional deficits, making the accuracy of tractography reconstructions paramount. The quality of dMRI tractography is influenced by many modifiable factors, ranging from MRI data acquisition through to the post-processing of tractography output, with the potential of error propagation based on decisions made at each and subsequent processing steps. Research over the last 25 years has significantly improved the anatomical accuracy of tractography. An updated review about tractography methodology in the context of neurosurgery is now timely given the thriving research activities in dMRI, to ensure more appropriate applications in the clinical neurosurgical realm. This article aims to review the dMRI physics, and tractography methodologies, highlighting recent advances to provide the key concepts of tractography-informed neurosurgery, with a focus on the general considerations, the current state of practice, technical challenges, potential advances, and future demands to this field.
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Affiliation(s)
- Joseph Yuan-Mou Yang
- Department of Neurosurgery, The Royal Children's Hospital, Melbourne, Australia.,Neuroscience Research, Murdoch Children's Research Institute, Melbourne, Australia.,Developmental Imaging, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Australia
| | - Chun-Hung Yeh
- Institute for Radiological Research, Chang Gung University and Chang Gung Memorial Hospital, Taoyuan, Taiwan.,Department of Child and Adolescent Psychiatry, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Cyril Poupon
- NeuroSpin, Frédéric Joliot Life Sciences Institute, CEA, CNRS, Paris-Saclay University, Gif-sur-Yvette, France
| | - Fernando Calamante
- The University of Sydney, Sydney Imaging, Sydney, Australia.,The University of Sydney, School of Biomedical Engineering, Sydney, Australia
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38
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Lucena O, Vos SB, Vakharia V, Duncan J, Ashkan K, Sparks R, Ourselin S. Enhancing the estimation of fiber orientation distributions using convolutional neural networks. Comput Biol Med 2021; 135:104643. [PMID: 34280774 DOI: 10.1016/j.compbiomed.2021.104643] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 07/07/2021] [Accepted: 07/07/2021] [Indexed: 11/17/2022]
Abstract
Local fiber orientation distributions (FODs) can be computed from diffusion magnetic resonance imaging (dMRI). The accuracy and ability of FODs to resolve complex fiber configurations benefits from acquisition protocols that sample a high number of gradient directions, a high maximum b-value, and multiple b-values. However, acquisition time and scanners that follow these standards are limited in clinical settings, often resulting in dMRI acquired at a single shell (single b-value). In this work, we learn improved FODs from clinically acquired dMRI. We evaluate patch-based 3D convolutional neural networks (CNNs) on their ability to regress multi-shell FODs from single-shell FODs, using constrained spherical deconvolution (CSD). We evaluate U-Net and High-Resolution Network (HighResNet) 3D CNN architectures on data from the Human Connectome Project and an in-house dataset. We evaluate how well each CNN can resolve FODs 1) when training and testing on datasets with the same dMRI acquisition protocol; 2) when testing on a dataset with a different dMRI acquisition protocol than used to train the CNN; and 3) when testing on a dataset with a fewer number of gradient directions than used to train the CNN. This work is a step towards more accurate FOD estimation in time- and resource-limited clinical environments.
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Affiliation(s)
- Oeslle Lucena
- School of Biomedical Engineering and Imaging Sciences, King's College London, UK.
| | - Sjoerd B Vos
- Centre for Medical Image Computing, Department of Computer Sciences, University College London, London, UK; Neuroradiological Academic Unit, University College London Queen Square Institute of Neurology, University College London, London, UK
| | - Vejay Vakharia
- Department of Clinical and Experimental Epilepsy, University College London, UK
| | - John Duncan
- Department of Clinical and Experimental Epilepsy, University College London, UK; National Hospital for Neurology and Neurosurgery, Queen Square, UK
| | | | - Rachel Sparks
- School of Biomedical Engineering and Imaging Sciences, King's College London, UK
| | - Sebastien Ourselin
- School of Biomedical Engineering and Imaging Sciences, King's College London, UK
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Feng Y, Song J, Yan W, Wang J, Zhao C, Zeng Q. Investigation of Local White Matter Properties in Professional Chess Player: A Diffusion Magnetic Resonance Imaging Study Based on Automatic Annotation Fiber Clustering. IEEE Trans Cogn Dev Syst 2021. [DOI: 10.1109/tcds.2020.2968116] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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40
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Sedghi A, O'Donnell LJ, Kapur T, Learned-Miller E, Mousavi P, Wells WM. Image registration: Maximum likelihood, minimum entropy and deep learning. Med Image Anal 2021; 69:101939. [PMID: 33388458 PMCID: PMC8046343 DOI: 10.1016/j.media.2020.101939] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 11/28/2020] [Accepted: 12/07/2020] [Indexed: 01/12/2023]
Abstract
In this work, we propose a theoretical framework based on maximum profile likelihood for pairwise and groupwise registration. By an asymptotic analysis, we demonstrate that maximum profile likelihood registration minimizes an upper bound on the joint entropy of the distribution that generates the joint image data. Further, we derive the congealing method for groupwise registration by optimizing the profile likelihood in closed form, and using coordinate ascent, or iterative model refinement. We also describe a method for feature based registration in the same framework and demonstrate it on groupwise tractographic registration. In the second part of the article, we propose an approach to deep metric registration that implements maximum likelihood registration using deep discriminative classifiers. We show further that this approach can be used for maximum profile likelihood registration to discharge the need for well-registered training data, using iterative model refinement. We demonstrate that the method succeeds on a challenging registration problem where the standard mutual information approach does not perform well.
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Affiliation(s)
- Alireza Sedghi
- Medical Informatics Laboratory, Queen's University, Kingston, Canada.
| | - Lauren J O'Donnell
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, USA
| | - Tina Kapur
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, USA
| | - Erik Learned-Miller
- College of Information and Computer Sciences, University of Massachusetts, Amherst, USA
| | - Parvin Mousavi
- Medical Informatics Laboratory, Queen's University, Kingston, Canada
| | - William M Wells
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Boston, USA
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41
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Jende JME, Kender Z, Mooshage C, Groener JB, Alvarez-Ramos L, Kollmer J, Juerchott A, Hahn A, Heiland S, Nawroth P, Bendszus M, Kopf S, Kurz FT. Diffusion Tensor Imaging of the Sciatic Nerve as a Surrogate Marker for Nerve Functionality of the Upper and Lower Limb in Patients With Diabetes and Prediabetes. Front Neurosci 2021; 15:642589. [PMID: 33746707 PMCID: PMC7966816 DOI: 10.3389/fnins.2021.642589] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/10/2021] [Indexed: 12/23/2022] Open
Abstract
Background Nerve damage in diabetic neuropathy (DN) is assumed to begin in the distal legs with a subsequent progression to hands and arms at later stages. In contrast, recent studies have found that lower limb nerve lesions in DN predominate at the proximal sciatic nerve and that, in the upper limb, nerve functions can be impaired at early stages of DN. Materials and Methods In this prospective, single-center cross-sectional study, participants underwent diffusion-weighted 3 Tesla magnetic resonance neurography in order to calculate the sciatic nerve’s fractional anisotropy (FA), a surrogate parameter for structural nerve integrity. Results were correlated with clinical and electrophysiological assessments of the lower limb and an examination of hand function derived from the Purdue Pegboard Test. Results Overall, 71 patients with diabetes, 11 patients with prediabetes and 25 age-matched control subjects took part in this study. In patients with diabetes, the sciatic nerve’s FA showed positive correlations with tibial and peroneal nerve conduction velocities (r = 0.62; p < 0.001 and r = 0.56; p < 0.001, respectively), and tibial and peroneal nerve compound motor action potentials (r = 0.62; p < 0.001 and r = 0.63; p < 0.001, respectively). Moreover, the sciatic nerve’s FA was correlated with the Pegboard Test results in patients with diabetes (r = 0.52; p < 0.001), prediabetes (r = 0.76; p < 0.001) and in controls (r = 0.79; p = 0.007). Conclusion This study is the first to show that the sciatic nerve’s FA is a surrogate marker for functional and electrophysiological parameters of both upper and lower limbs in patients with diabetes and prediabetes, suggesting that nerve damage in these patients is not restricted to the level of the symptomatic limbs but rather affects the entire peripheral nervous system.
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Affiliation(s)
- Johann M E Jende
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Zoltan Kender
- Department of Endocrinology, Diabetology and Clinical Chemistry, Heidelberg University Hospital, Heidelberg, Germany
| | - Christoph Mooshage
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Jan B Groener
- Department of Endocrinology, Diabetology and Clinical Chemistry, Heidelberg University Hospital, Heidelberg, Germany.,Medicover Neuroendocrinology, Munich, Germany.,German Center of Diabetes Research (DZD), Associated Partner in the DZD, München-Neuherberg, Germany
| | - Lucia Alvarez-Ramos
- Department of Endocrinology, Diabetology and Clinical Chemistry, Heidelberg University Hospital, Heidelberg, Germany
| | - Jennifer Kollmer
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Alexander Juerchott
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Artur Hahn
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Sabine Heiland
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany.,Division of Experimental Radiology, Department of Neuroradiology, Heidelberg, Germany
| | - Peter Nawroth
- Department of Endocrinology, Diabetology and Clinical Chemistry, Heidelberg University Hospital, Heidelberg, Germany.,German Center of Diabetes Research (DZD), Associated Partner in the DZD, München-Neuherberg, Germany.,Joint Institute for Diabetes and Cancer at Helmholtz-Zentrum Munich and Heidelberg University, Heidelberg, Germany
| | - Martin Bendszus
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan Kopf
- Department of Endocrinology, Diabetology and Clinical Chemistry, Heidelberg University Hospital, Heidelberg, Germany.,German Center of Diabetes Research (DZD), Associated Partner in the DZD, München-Neuherberg, Germany
| | - Felix T Kurz
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
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Liheng M, Guofan X, Balzano RF, Yuying L, Weifeng H, Ning Y, Yayun J, Mouyuan L, Guglielmi G. The value of DTI: achieving high diagnostic performance for brain metastasis. LA RADIOLOGIA MEDICA 2021; 126:291-298. [PMID: 32564269 DOI: 10.1007/s11547-020-01243-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 06/08/2020] [Indexed: 12/08/2022]
Abstract
BACKGROUND The evaluation of brain metastases generally requires post-contrast MRI exam, but some patients have contraindication to contrast medium administration. PURPOSE To investigate the value of the MRI diffusion tensor imaging (DTI) for detection of metastatic brain tumor. MATERIALS AND METHODS We retrospectively analyzed the MRI data from 23 patients (13 males and 10 females) with brain metastases. The MRI protocol consisted in T1WI, T2WI, post-contrast 3DT1WI and DTI images (b = 1000) sequences. The brain metastatic lesions were counted in each of these sequences. We compared the advantages and limitations of different sequences in the brain metastases detection. The number of metastatic lesions identified on the contrast-enhanced 3DT1WI image is used as the reference. FA values were measured in the intratumoral, adjacent peritumoral and distant peritumoral edema area (PTEA) of brain metastasis, and the differences were statistically analyzed. RESULTS DTI can detect more brain metastatic lesions rather than T1WI and T2WI. The number of brain metastases on DTI is similar to post-contrast 3D T1WI. There is no statistical difference in the FA value change between the adjacent and distant PTEA. CONCLUSION The DTI original image can be used as an alternative examination for patients with contraindications to contrast-enhanced MRI. It has high sensitivity to intratumoral hemorrhage, which has advantage to detect brain metastatic lesions as compared with T1WI or T2WI images.
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Affiliation(s)
- Ma Liheng
- Imaging Department, First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou City, Guangdong Province, China
| | - Xu Guofan
- Division of Diagnostic Imaging, Department of Nuclear Medicine and Imaging Physics, MD Anderson Cancer Center, Houston City, TX, USA
| | - Rosario Francesco Balzano
- Department of Clinical and Experimental Medicine, University School of Medicine, Viale L. Pinto, 1, 71121, Foggia, Italy
| | - Liang Yuying
- Imaging Department, First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou City, Guangdong Province, China
| | - Hong Weifeng
- Imaging Department, First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou City, Guangdong Province, China
| | - Yang Ning
- Pathology Department, First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou City, Guangdong Province, China
| | - Ji Yayun
- Imaging Department, First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou City, Guangdong Province, China
| | - Liu Mouyuan
- Imaging Department, First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou City, Guangdong Province, China
| | - Giuseppe Guglielmi
- Department of Clinical and Experimental Medicine, University School of Medicine, Viale L. Pinto, 1, 71121, Foggia, Italy.
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43
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Henderson F, Abdullah KG, Verma R, Brem S. Tractography and the connectome in neurosurgical treatment of gliomas: the premise, the progress, and the potential. Neurosurg Focus 2021; 48:E6. [PMID: 32006950 DOI: 10.3171/2019.11.focus19785] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 11/13/2019] [Indexed: 12/21/2022]
Abstract
The ability of diffusion tensor MRI to detect the preferential diffusion of water in cerebral white matter tracts enables neurosurgeons to noninvasively visualize the relationship of lesions to functional neural pathways. Although viewed as a research tool in its infancy, diffusion tractography has evolved into a neurosurgical tool with applications in glioma surgery that are enhanced by evolutions in crossing fiber visualization, edema correction, and automated tract identification. In this paper the current literature supporting the use of tractography in brain tumor surgery is summarized, highlighting important clinical studies on the application of diffusion tensor imaging (DTI) for preoperative planning of glioma resection, and risk assessment to analyze postoperative outcomes. The key methods of tractography in current practice and crucial white matter fiber bundles are summarized. After a review of the physical basis of DTI and post-DTI tractography, the authors discuss the methodologies with which to adapt DT image processing for surgical planning, as well as the potential of connectomic imaging to facilitate a network approach to oncofunctional optimization in glioma surgery.
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Affiliation(s)
- Fraser Henderson
- 1Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania.,3Department of Neurosurgery, The Medical University of South Carolina, Charleston, South Carolina; and
| | - Kalil G Abdullah
- 4Department of Neurosurgery, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Ragini Verma
- 1Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania.,2DiCIPHR (Diffusion and Connectomics in Precision Healthcare Research) Lab, Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Steven Brem
- 1Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania
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Steinmann S, Lyall AE, Langhein M, Nägele FL, Rauh J, Cetin-Karayumak S, Zhang F, Mussmann M, Billah T, Makris N, Pasternak O, O'Donnell LJ, Rathi Y, Kubicki M, Leicht G, Shenton ME, Mulert C. Sex-Related Differences in White Matter Asymmetry and Its Implications for Verbal Working Memory in Psychosis High-Risk State. Front Psychiatry 2021; 12:686967. [PMID: 34194350 PMCID: PMC8236502 DOI: 10.3389/fpsyt.2021.686967] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 05/17/2021] [Indexed: 12/19/2022] Open
Abstract
Objective: Sexual dimorphism has been investigated in schizophrenia, although sex-specific differences among individuals who are at clinical high-risk (CHR) for developing psychosis have been inconclusive. This study aims to characterize sexual dimorphism of language areas in the brain by investigating the asymmetry of four white matter tracts relevant to verbal working memory in CHR patients compared to healthy controls (HC). HC typically show a leftward asymmetry of these tracts. Moreover, structural abnormalities in asymmetry and verbal working memory dysfunctions have been associated with neurodevelopmental abnormalities and are considered core features of schizophrenia. Methods: Twenty-nine subjects with CHR (17 female/12 male) for developing psychosis and twenty-one HC (11 female/10 male) matched for age, sex, and education were included in the study. Two-tensor unscented Kalman filter tractography, followed by an automated, atlas-guided fiber clustering approach, were used to identify four fiber tracts related to verbal working memory: the superior longitudinal fasciculi (SLF) I, II and III, and the superior occipitofrontal fasciculus (SOFF). Using fractional anisotropy (FA) of tissue as the primary measure, we calculated the laterality index for each tract. Results: There was a significantly greater right>left asymmetry of the SLF-III in CHR females compared to HC females, but no hemispheric difference between CHR vs. HC males. Moreover, the laterality index of SLF-III for CHR females correlated negatively with Backward Digit Span performance, suggesting a greater rightward asymmetry was associated with poorer working memory functioning. Conclusion: This study suggests increased rightward asymmetry of the SLF-III in CHR females. This finding of sexual dimorphism in white matter asymmetry in a language-related area of the brain in CHR highlights the need for a deeper understanding of the role of sex in the high-risk state. Future work investigating early sex-specific pathophysiological mechanisms, may lead to the development of novel personalized treatment strategies aimed at preventing transition to a more chronic and difficult-to-treat disorder.
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Affiliation(s)
- Saskia Steinmann
- Psychiatry Neuroimaging Branch, Department of Psychiatry and Psychotherapy, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Boston, MA, United States
| | - Amanda E Lyall
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Boston, MA, United States.,Department of Psychiatry, Massachusetts General Hospital Harvard Medical School, Boston, MA, United States
| | - Mina Langhein
- Psychiatry Neuroimaging Branch, Department of Psychiatry and Psychotherapy, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Boston, MA, United States
| | - Felix L Nägele
- Psychiatry Neuroimaging Branch, Department of Psychiatry and Psychotherapy, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jonas Rauh
- Psychiatry Neuroimaging Branch, Department of Psychiatry and Psychotherapy, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Suheyla Cetin-Karayumak
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Boston, MA, United States
| | - Fan Zhang
- Department of Radiology, Brigham and Women's Hospital Harvard Medical School, Boston, MA, United States
| | - Marius Mussmann
- Psychiatry Neuroimaging Branch, Department of Psychiatry and Psychotherapy, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tashrif Billah
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Boston, MA, United States
| | - Nikos Makris
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Boston, MA, United States.,Department of Psychiatry, Massachusetts General Hospital Harvard Medical School, Boston, MA, United States
| | - Ofer Pasternak
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Boston, MA, United States.,Department of Radiology, Brigham and Women's Hospital Harvard Medical School, Boston, MA, United States
| | - Lauren J O'Donnell
- Department of Radiology, Brigham and Women's Hospital Harvard Medical School, Boston, MA, United States
| | - Yogesh Rathi
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Boston, MA, United States.,Department of Radiology, Brigham and Women's Hospital Harvard Medical School, Boston, MA, United States
| | - Marek Kubicki
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Boston, MA, United States.,Department of Psychiatry, Massachusetts General Hospital Harvard Medical School, Boston, MA, United States
| | - Gregor Leicht
- Psychiatry Neuroimaging Branch, Department of Psychiatry and Psychotherapy, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martha E Shenton
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Boston, MA, United States.,Department of Psychiatry, Massachusetts General Hospital Harvard Medical School, Boston, MA, United States.,Department of Radiology, Brigham and Women's Hospital Harvard Medical School, Boston, MA, United States
| | - Christoph Mulert
- Psychiatry Neuroimaging Branch, Department of Psychiatry and Psychotherapy, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Center for Psychiatry and Psychotherapy, Justus-Liebig-University Giessen, Giessen, Germany
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45
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Zhong L, Li T, Shu H, Huang C, Michael Johnson J, Schomer DF, Liu HL, Feng Q, Yang W, Zhu H. (TS) 2WM: Tumor Segmentation and Tract Statistics for Assessing White Matter Integrity with Applications to Glioblastoma Patients. Neuroimage 2020; 223:117368. [PMID: 32931941 PMCID: PMC7688588 DOI: 10.1016/j.neuroimage.2020.117368] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 08/23/2020] [Accepted: 09/08/2020] [Indexed: 11/24/2022] Open
Abstract
Glioblastoma (GBM) brain tumor is the most aggressive white matter (WM) invasive cerebral primary neoplasm. Due to its inherently heterogeneous appearance and shape, previous studies pursued either the segmentation precision of the tumors or qualitative analysis of the impact of brain tumors on WM integrity with manual delineation of tumors. This paper aims to develop a comprehensive analytical pipeline, called (TS)2WM, to integrate both the superior performance of brain tumor segmentation and the impact of GBM tumors on the WM integrity via tumor segmentation and tract statistics using the diffusion tensor imaging (DTI) technique. The (TS)2WM consists of three components: (i) A dilated densely connected convolutional network (D2C2N) for automatically segment GBM tumors. (ii) A modified structural connectome processing pipeline to characterize the connectivity pattern of WM bundles. (iii) A multivariate analysis to delineate the local and global associations between different DTI-related measurements and clinical variables on both brain tumors and language-related regions of interest. Among those, the proposed D2C2N model achieves competitive tumor segmentation accuracy compared with many state-of-the-art tumor segmentation methods. Significant differences in various DTI-related measurements at the streamline, weighted network, and binary network levels (e.g., diffusion properties along major fiber bundles) were found in tumor-related, language-related, and hand motor-related brain regions in 62 GBM patients as compared to healthy subjects from the Human Connectome Project.
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Affiliation(s)
- Liming Zhong
- Guangdong Provincial Key Laboratory of Medical Image Processing, School of Biomedical Engineering, Southern Medical University, Guangzhou, China
| | - Tengfei Li
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States; Department of Radiology and Biomedical Research Imaging Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States
| | - Hai Shu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States; Department of Biostatistics, School of Global Public Health, New York University, New York, United States
| | - Chao Huang
- Department of Statistics, Florida State University, Tallahassee, FL, United States
| | - Jason Michael Johnson
- Department of Diagnostic Radiology, Division of Diagnostic Imaging, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States
| | - Donald F Schomer
- Department of Diagnostic Radiology, Division of Diagnostic Imaging, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States
| | - Ho-Ling Liu
- Department of Imaging Physics, Division of Diagnostic Imaging, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States
| | - Qianjin Feng
- Guangdong Provincial Key Laboratory of Medical Image Processing, School of Biomedical Engineering, Southern Medical University, Guangzhou, China
| | - Wei Yang
- Guangdong Provincial Key Laboratory of Medical Image Processing, School of Biomedical Engineering, Southern Medical University, Guangzhou, China
| | - Hongtu Zhu
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States; Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States; Department of Radiology and Biomedical Research Imaging Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States.
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46
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Zhang F, Xie G, Leung L, Mooney MA, Epprecht L, Norton I, Rathi Y, Kikinis R, Al-Mefty O, Makris N, Golby AJ, O'Donnell LJ. Creation of a novel trigeminal tractography atlas for automated trigeminal nerve identification. Neuroimage 2020; 220:117063. [PMID: 32574805 PMCID: PMC7572753 DOI: 10.1016/j.neuroimage.2020.117063] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/07/2020] [Accepted: 06/14/2020] [Indexed: 12/29/2022] Open
Abstract
Diffusion MRI (dMRI) tractography has been successfully used to study the trigeminal nerves (TGNs) in many clinical and research applications. Currently, identification of the TGN in tractography data requires expert nerve selection using manually drawn regions of interest (ROIs), which is prone to inter-observer variability, time-consuming and carries high clinical and labor costs. To overcome these issues, we propose to create a novel anatomically curated TGN tractography atlas that enables automated identification of the TGN from dMRI tractography. In this paper, we first illustrate the creation of a trigeminal tractography atlas. Leveraging a well-established computational pipeline and expert neuroanatomical knowledge, we generate a data-driven TGN fiber clustering atlas using tractography data from 50 subjects from the Human Connectome Project. Then, we demonstrate the application of the proposed atlas for automated TGN identification in new subjects, without relying on expert ROI placement. Quantitative and visual experiments are performed with comparison to expert TGN identification using dMRI data from two different acquisition sites. We show highly comparable results between the automatically and manually identified TGNs in terms of spatial overlap and visualization, while our proposed method has several advantages. First, our method performs automated TGN identification, and thus it provides an efficient tool to reduce expert labor costs and inter-operator bias relative to expert manual selection. Second, our method is robust to potential imaging artifacts and/or noise that can prevent successful manual ROI placement for TGN selection and hence yields a higher successful TGN identification rate.
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Affiliation(s)
- Fan Zhang
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, USA.
| | - Guoqiang Xie
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, USA; Department of Neurosurgery, Nuclear Industry 215 Hospital of Shaanxi Province, Xianyang, China
| | - Laura Leung
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, USA; Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, USA; Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Michael A Mooney
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, USA
| | - Lorenz Epprecht
- Department of Otolaryngology, Head and Neck Surgery, University Hospital Zurich, Zurich, Switzerland
| | - Isaiah Norton
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, USA
| | - Yogesh Rathi
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, USA; Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, USA
| | - Ron Kikinis
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, USA
| | - Ossama Al-Mefty
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, USA
| | - Nikos Makris
- Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, USA; Departments of Psychiatry, Neurology and Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, USA
| | - Alexandra J Golby
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, USA; Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, USA
| | - Lauren J O'Donnell
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, USA
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47
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Zhang F, Cetin Karayumak S, Hoffmann N, Rathi Y, Golby AJ, O'Donnell LJ. Deep white matter analysis (DeepWMA): Fast and consistent tractography segmentation. Med Image Anal 2020; 65:101761. [PMID: 32622304 PMCID: PMC7483951 DOI: 10.1016/j.media.2020.101761] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 06/16/2020] [Accepted: 06/18/2020] [Indexed: 02/07/2023]
Abstract
White matter tract segmentation, i.e. identifying tractography fibers (streamline trajectories) belonging to anatomically meaningful fiber tracts, is an essential step to enable tract quantification and visualization. In this study, we present a deep learning tractography segmentation method (DeepWMA) that allows fast and consistent identification of 54 major deep white matter fiber tracts from the whole brain. We create a large-scale training tractography dataset of 1 million labeled fiber samples, and we propose a novel 2D multi-channel feature descriptor (FiberMap) that encodes spatial coordinates of points along each fiber. We learn a convolutional neural network (CNN) fiber classification model based on FiberMap and obtain a high fiber classification accuracy of 90.99% on the training tractography data with ground truth fiber labels. Then, the method is evaluated on a test dataset of 597 diffusion MRI scans from six independently acquired populations across genders, the lifespan (1 day - 82 years), and different health conditions (healthy control, neuropsychiatric disorders, and brain tumor patients). We perform comparisons with two state-of-the-art tract segmentation methods. Experimental results show that our method obtains a highly consistent tract segmentation result, where on average over 99% of the fiber tracts are successfully identified across all subjects under study, most importantly, including neonates and patients with space-occupying brain tumors. We also demonstrate good generalization of the method to tractography data from multiple different fiber tracking methods. The proposed method leverages deep learning techniques and provides a fast and efficient tool for brain white matter segmentation in large diffusion MRI tractography datasets.
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Affiliation(s)
- Fan Zhang
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | | | - Nico Hoffmann
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yogesh Rathi
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Alexandra J Golby
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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48
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Bertò G, Bullock D, Astolfi P, Hayashi S, Zigiotto L, Annicchiarico L, Corsini F, De Benedictis A, Sarubbo S, Pestilli F, Avesani P, Olivetti E. Classifyber, a robust streamline-based linear classifier for white matter bundle segmentation. Neuroimage 2020; 224:117402. [PMID: 32979520 DOI: 10.1016/j.neuroimage.2020.117402] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 09/12/2020] [Accepted: 09/18/2020] [Indexed: 12/18/2022] Open
Abstract
Virtual delineation of white matter bundles in the human brain is of paramount importance for multiple applications, such as pre-surgical planning and connectomics. A substantial body of literature is related to methods that automatically segment bundles from diffusion Magnetic Resonance Imaging (dMRI) data indirectly, by exploiting either the idea of connectivity between regions or the geometry of fiber paths obtained with tractography techniques, or, directly, through the information in volumetric data. Despite the remarkable improvement in automatic segmentation methods over the years, their segmentation quality is not yet satisfactory, especially when dealing with datasets with very diverse characteristics, such as different tracking methods, bundle sizes or data quality. In this work, we propose a novel, supervised streamline-based segmentation method, called Classifyber, which combines information from atlases, connectivity patterns, and the geometry of fiber paths into a simple linear model. With a wide range of experiments on multiple datasets that span from research to clinical domains, we show that Classifyber substantially improves the quality of segmentation as compared to other state-of-the-art methods and, more importantly, that it is robust across very diverse settings. We provide an implementation of the proposed method as open source code, as well as web service.
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Affiliation(s)
- Giulia Bertò
- NeuroInformatics Laboratory (NILab), Bruno Kessler Foundation (FBK), Trento, Italy; Center for Mind and Brain Sciences (CIMeC), University of Trento, Italy
| | - Daniel Bullock
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, USA
| | - Pietro Astolfi
- NeuroInformatics Laboratory (NILab), Bruno Kessler Foundation (FBK), Trento, Italy; Center for Mind and Brain Sciences (CIMeC), University of Trento, Italy; PAVIS, Italian Institute of Technology (IIT), Genova, Italy
| | - Soichi Hayashi
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, USA
| | - Luca Zigiotto
- Division of Neurosurgery, Structural and Functional Connectivity Lab, S. Chiara Hospital, Trento, Italy
| | - Luciano Annicchiarico
- Division of Neurosurgery, Structural and Functional Connectivity Lab, S. Chiara Hospital, Trento, Italy
| | - Francesco Corsini
- Division of Neurosurgery, Structural and Functional Connectivity Lab, S. Chiara Hospital, Trento, Italy
| | - Alessandro De Benedictis
- Neurosurgery Unit, Department of Neuroscience, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Silvio Sarubbo
- Division of Neurosurgery, Structural and Functional Connectivity Lab, S. Chiara Hospital, Trento, Italy
| | - Franco Pestilli
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, USA
| | - Paolo Avesani
- NeuroInformatics Laboratory (NILab), Bruno Kessler Foundation (FBK), Trento, Italy; Center for Mind and Brain Sciences (CIMeC), University of Trento, Italy
| | - Emanuele Olivetti
- NeuroInformatics Laboratory (NILab), Bruno Kessler Foundation (FBK), Trento, Italy; Center for Mind and Brain Sciences (CIMeC), University of Trento, Italy.
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49
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Wang J, Zhang F, Zhao C, Zeng Q, He J, O'Donnell LJ, Feng Y. Investigation of local white matter abnormality in Parkinson's disease by using an automatic fiber tract parcellation. Behav Brain Res 2020; 394:112805. [PMID: 32673707 DOI: 10.1016/j.bbr.2020.112805] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 07/01/2020] [Accepted: 07/08/2020] [Indexed: 11/18/2022]
Abstract
The deficits of white matter (WM) microstructure are involved during Parkinson's disease (PD) progression. Most current methods identify key WM tracts relying on cortical regions of interest (ROIs). However, such ROI methods can be challenged due to low diffusion anisotropy near the gray matter (GM), which could result in a low sensitivity of tract identification. This work proposes an automatic WM parcellation method to improve the accuracy of WM tract identification and locate abnormal tracts by using sensitive features. The proposed method consists of 1) whole brain WM parcellation using an established fiber clustering method, without using any ROIs, 2) features of fasciculus were calculated to quantify diffusion measures at each equal cross-section along the whole cluster. Then, we use the proposed features to investigate the WM difference in PD compared with healthy controls (HC). We also use these features to investigate the relationship of clinical symptoms and specific fiber tracts. The novelty of the proposed method is that it automatically identifies the abnormal WM fibers in cluster degree. Experiment results indicated that the proposed method had advantage in detecting the local WM abnormality by performing between-group statistical analysis in 30 patients with PD and 28 HC. We found 13 hemisphere clusters and 8 commissural clusters had significant group difference (p < 0.05, corrected by FDR method) in local regions, which belonged to multiple fiber tracts including cingulum bundle (CB), inferior occipito-frontal fasciculus (IoFF), corpus callosum (CC), external capsule (EC), uncinate fasciculus (UF), superior longitudinal fasciculus (SLF) and thalamo front (TF). We also found clusters that had relevance with clinical indices of cognitive function (2 clusters), athletic function (6 clusters), and depressive state (2 clusters) in these significant clusters. From the experiment results, it confirmed the ability of the proposed method to identify potential WM microstructure abnormality.
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Affiliation(s)
- Jingqiang Wang
- College of Information Engineering, Zhejiang University of Technology, Hangzhou, China
| | - Fan Zhang
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Changchen Zhao
- College of Information Engineering, Zhejiang University of Technology, Hangzhou, China
| | - Qingrun Zeng
- College of Information Engineering, Zhejiang University of Technology, Hangzhou, China
| | - Jianzhong He
- College of Information Engineering, Zhejiang University of Technology, Hangzhou, China
| | | | - Yuanjing Feng
- College of Information Engineering, Zhejiang University of Technology, Hangzhou, China
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50
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Vázquez A, López-López N, Sánchez A, Houenou J, Poupon C, Mangin JF, Hernández C, Guevara P. FFClust: Fast fiber clustering for large tractography datasets for a detailed study of brain connectivity. Neuroimage 2020; 220:117070. [PMID: 32599269 DOI: 10.1016/j.neuroimage.2020.117070] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 03/19/2020] [Accepted: 06/16/2020] [Indexed: 01/31/2023] Open
Abstract
Automated methods that can identify white matter bundles from large tractography datasets have several applications in neuroscience research. In these applications, clustering algorithms have shown to play an important role in the analysis and visualization of white matter structure, generating useful data which can be the basis for further studies. This work proposes FFClust, an efficient fiber clustering method for large tractography datasets containing millions of fibers. Resulting clusters describe the whole set of main white matter fascicles present on an individual brain. The method aims to identify compact and homogeneous clusters, which enables several applications. In individuals, the clusters can be used to study the local connectivity in pathological brains, while at population level, the processing and analysis of reproducible bundles, and other post-processing algorithms can be carried out to study the brain connectivity and create new white matter bundle atlases. The proposed method was evaluated in terms of quality and execution time performance versus the state-of-the-art clustering techniques used in the area. Results show that FFClust is effective in the creation of compact clusters, with a low intra-cluster distance, while keeping a good quality Davies-Bouldin index, which is a metric that quantifies the quality of clustering approaches. Furthermore, it is about 8.6 times faster than the most efficient state-of-the-art method for one million fibers dataset. In addition, we show that FFClust is able to correctly identify atlas bundles connecting different brain regions, as an example of application and the utility of compact clusters.
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Affiliation(s)
- Andrea Vázquez
- Universidad de Concepción, Department of Computer Science, Concepción, Chile
| | - Narciso López-López
- Universidad de Concepción, Department of Computer Science, Concepción, Chile; Universidade da Coruña, Centro de investigación CITIC, A Coruña, Spain
| | - Alexis Sánchez
- Universidad de Concepción, Department of Computer Science, Concepción, Chile
| | - Josselin Houenou
- Université Paris-Saclay, CEA, CNRS, Baobab, Neurospin, Gif-sur-Yvette, France; INSERM U955 Unit, Mondor Institute for Biomedical Research, Team 15 "Translational Psychiatry", Créteil, France; Fondation Fondamental, Créteil, France; AP-HP, Department of Psychiatry and Addictology, Mondor University Hospitals, School of Medicine, DHU PePsy, Créteil, France
| | - Cyril Poupon
- Université Paris-Saclay, CEA, CNRS, Baobab, Neurospin, Gif-sur-Yvette, France
| | | | - Cecilia Hernández
- Universidad de Concepción, Department of Computer Science, Concepción, Chile; Center for Biotechnology and Bioengineering (CeBiB), Santiago, Chile
| | - Pamela Guevara
- Universidad de Concepción, Department of Electrical Engineering, Concepción, Chile.
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