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Kontopodis EE, Papadaki E, Trivizakis E, Maris TG, Simos P, Papadakis GZ, Tsatsakis A, Spandidos DA, Karantanas A, Marias K. Emerging deep learning techniques using magnetic resonance imaging data applied in multiple sclerosis and clinical isolated syndrome patients (Review). Exp Ther Med 2021; 22:1149. [PMID: 34504594 PMCID: PMC8393268 DOI: 10.3892/etm.2021.10583] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 07/29/2021] [Indexed: 12/18/2022] Open
Abstract
Computer-aided diagnosis systems aim to assist clinicians in the early identification of abnormal signs in order to optimize the interpretation of medical images and increase diagnostic precision. Multiple sclerosis (MS) and clinically isolated syndrome (CIS) are chronic inflammatory, demyelinating diseases affecting the central nervous system. Recent advances in deep learning (DL) techniques have led to novel computational paradigms in MS and CIS imaging designed for automatic segmentation and detection of areas of interest and automatic classification of anatomic structures, as well as optimization of neuroimaging protocols. To this end, there are several publications presenting artificial intelligence-based predictive models aiming to increase diagnostic accuracy and to facilitate optimal clinical management in patients diagnosed with MS and/or CIS. The current study presents a thorough review covering DL techniques that have been applied in MS and CIS during recent years, shedding light on their current advances and limitations.
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Affiliation(s)
- Eleftherios E Kontopodis
- Computational BioMedicine Laboratory, Institute of Computer Science, Foundation for Research and Technology-Hellas, 70013 Heraklion, Greece.,Department of Radiology, Medical School, University of Crete, 70013 Heraklion, Greece
| | - Efrosini Papadaki
- Computational BioMedicine Laboratory, Institute of Computer Science, Foundation for Research and Technology-Hellas, 70013 Heraklion, Greece.,Department of Radiology, Medical School, University of Crete, 70013 Heraklion, Greece
| | - Eleftherios Trivizakis
- Computational BioMedicine Laboratory, Institute of Computer Science, Foundation for Research and Technology-Hellas, 70013 Heraklion, Greece.,Department of Radiology, Medical School, University of Crete, 70013 Heraklion, Greece
| | - Thomas G Maris
- Computational BioMedicine Laboratory, Institute of Computer Science, Foundation for Research and Technology-Hellas, 70013 Heraklion, Greece.,Department of Radiology, Medical School, University of Crete, 70013 Heraklion, Greece
| | - Panagiotis Simos
- Computational BioMedicine Laboratory, Institute of Computer Science, Foundation for Research and Technology-Hellas, 70013 Heraklion, Greece.,Department of Psychiatry and Behavioral Sciences, Medical School, University of Crete, 70013 Heraklion, Greece
| | - Georgios Z Papadakis
- Computational BioMedicine Laboratory, Institute of Computer Science, Foundation for Research and Technology-Hellas, 70013 Heraklion, Greece.,Department of Radiology, Medical School, University of Crete, 70013 Heraklion, Greece
| | - Aristidis Tsatsakis
- Centre of Toxicology Science and Research, Faculty of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Demetrios A Spandidos
- Laboratory of Clinical Virology, Medical School, University of Crete, 71003 Heraklion, Greece
| | - Apostolos Karantanas
- Computational BioMedicine Laboratory, Institute of Computer Science, Foundation for Research and Technology-Hellas, 70013 Heraklion, Greece.,Department of Radiology, Medical School, University of Crete, 70013 Heraklion, Greece
| | - Kostas Marias
- Computational BioMedicine Laboratory, Institute of Computer Science, Foundation for Research and Technology-Hellas, 70013 Heraklion, Greece.,Department of Electrical and Computer Engineering, Hellenic Mediterranean University, 71410 Heraklion, Greece
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Gregory S, Lohse KR, Johnson EB, Leavitt BR, Durr A, Roos RAC, Rees G, Tabrizi SJ, Scahill RI, Orth M. Longitudinal Structural MRI in Neurologically Healthy Adults. J Magn Reson Imaging 2020; 52:1385-1399. [PMID: 32469154 PMCID: PMC8425332 DOI: 10.1002/jmri.27203] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/07/2020] [Accepted: 05/07/2020] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Structural brain MRI measures are frequently examined in both healthy and clinical groups, so an understanding of how these measures vary over time is desirable. PURPOSE To test the stability of structural brain MRI measures over time. POPULATION In all, 112 healthy volunteers across four sites. STUDY TYPE Retrospective analysis of prospectively acquired data. FIELD STRENGTH/SEQUENCE 3 T, magnetization prepared - rapid gradient echo, and single-shell diffusion sequence. ASSESSMENT Diffusion, cortical thickness, and volume data from the sensorimotor network were assessed for stability over time across 3 years. Two sites used a Siemens MRI scanner, two sites a Philips scanner. STATISTICAL TESTS The stability of structural measures across timepoints was assessed using intraclass correlation coefficients (ICC) for absolute agreement, cutoff ≥0.80, indicating high reliability. Mixed-factorial analysis of variance (ANOVA) was used to examine between-site and between-scanner type differences in individuals over time. RESULTS All cortical thickness and gray matter volume measures in the sensorimotor network, plus all diffusivity measures (fractional anisotropy plus mean, axial and radial diffusivities) for primary and premotor cortices, primary somatosensory thalamic connections, and the cortico-spinal tract met ICC. The majority of measures differed significantly between scanners, with a trend for sites using Siemens scanners to produce larger values for connectivity, cortical thickness, and volume measures than sites using Philips scanners. DATA CONCLUSION Levels of reliability over time for all tested structural MRI measures were generally high, indicating that any differences between measurements over time likely reflect underlying biological differences rather than inherent methodological variability. LEVEL OF EVIDENCE 4. TECHNICAL EFFICACY STAGE 1.
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Affiliation(s)
- Sarah Gregory
- Huntington's Disease Research Centre, Institute of Neurology, University College London, London, UK.,Wellcome Centre for Human Neuroimaging, Institute of Neurology, University College London, London, UK
| | - Keith R Lohse
- Department of Health, Kinesiology, and Recreation, University of Utah, Salt Lake City, Utah, USA.,Department of Physical Therapy and Athletic Training, University of Utah, Salt Lake City, Utah, USA
| | - Eileanoir B Johnson
- Huntington's Disease Research Centre, Institute of Neurology, University College London, London, UK
| | - Blair R Leavitt
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alexandra Durr
- APHP Department of Genetics, Pitié-Salpêtrière University Hospital, and Institut du Cerveau et de la Moell épinière (ICM), Sorbonne Université, Paris, France
| | - Raymund A C Roos
- Department of Neurology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Geraint Rees
- Wellcome Centre for Human Neuroimaging, Institute of Neurology, University College London, London, UK.,Institute of Cognitive Neuroscience, University College London, London, UK
| | - Sarah J Tabrizi
- Huntington's Disease Research Centre, Institute of Neurology, University College London, London, UK
| | - Rachael I Scahill
- Huntington's Disease Research Centre, Institute of Neurology, University College London, London, UK
| | - Michael Orth
- Department of Neurology, Ulm University Hospital, Ulm, Germany.,Neurozentrum Siloah, Bern, Switzerland
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Abolhasani Foroughi A, Salahi R, Nikseresht A, Heidari H, Nazeri M, Khorsand A. Comparison of diffusion-weighted imaging and enhanced T1-weighted sequencing in patients with multiple sclerosis. Neuroradiol J 2017; 30:347-351. [PMID: 28452571 DOI: 10.1177/1971400916678224] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Introduction The purpose of this study was to assess whether demographic, brain anatomical regions and contrast enhancement show differences in multiple sclerosis (MS) patients with increased diffusion lesions (ID group) compared with diffusion restriction (DR group). Method MRI protocol comprised T1- and T2-weighted sequences with and without gadolinium (Gd), and sagittal three-dimensional FLAIR sequence, DWI and ADC maps were prospectively performed in 126 MS patients from January to December 2015. The investigation was conducted to evaluate differences in demographic, cord and brain regional, technical, and positive or negative Gd contrast imaging parameters in two groups of ID and DR. Statistical analysis was performed by using SPSS. Results A total of 9.6% of patients showed DR. In the DR group, 66.6% of the patients showed contrast enhancement of plaques, whereas 29.2% of the IR group showed enhancement of plaques. The most prevalent group was non-enhanced plaques in the ID group, followed by Gd-enhanced plaques in the ID group. Patients in the ID group (90.4%) were significantly more than in the DR group (9.6%). Out of the 40 patients with Gd-enhanced plaques, 80.5% was from the ID group and 19.5% from the DR group. Conclusion MRI of the brain, unlike of the cord, with Gd demonstrates significant difference in enhancement between the two groups ( p < 0.05). No significant difference was seen in demographic, cord and brain regional, and technical parameters, EDSS, disease duration, and attack rate as well as demographic and regional parameters between the ID and decrease diffusion groups ( p > 0.05).
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Affiliation(s)
- Amin Abolhasani Foroughi
- 1 Medical Imaging Research Center, Department of Radiology, Shiraz University of Medical Sciences, Shiraz Iran
| | - Roohollah Salahi
- 1 Medical Imaging Research Center, Department of Radiology, Shiraz University of Medical Sciences, Shiraz Iran
| | - Alireza Nikseresht
- 2 Clinical Neurology Research Center, Department of Neurology, Shiraz University of Medical Sciences, Shiraz Iran
| | - Hora Heidari
- 2 Clinical Neurology Research Center, Department of Neurology, Shiraz University of Medical Sciences, Shiraz Iran
| | - Masoume Nazeri
- 2 Clinical Neurology Research Center, Department of Neurology, Shiraz University of Medical Sciences, Shiraz Iran
| | - Ali Khorsand
- 1 Medical Imaging Research Center, Department of Radiology, Shiraz University of Medical Sciences, Shiraz Iran
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Zaimi A, Duval T, Gasecka A, Côté D, Stikov N, Cohen-Adad J. AxonSeg: Open Source Software for Axon and Myelin Segmentation and Morphometric Analysis. Front Neuroinform 2016; 10:37. [PMID: 27594833 PMCID: PMC4990549 DOI: 10.3389/fninf.2016.00037] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 08/08/2016] [Indexed: 01/21/2023] Open
Abstract
Segmenting axon and myelin from microscopic images is relevant for studying the peripheral and central nervous system and for validating new MRI techniques that aim at quantifying tissue microstructure. While several software packages have been proposed, their interface is sometimes limited and/or they are designed to work with a specific modality (e.g., scanning electron microscopy (SEM) only). Here we introduce AxonSeg, which allows to perform automatic axon and myelin segmentation on histology images, and to extract relevant morphometric information, such as axon diameter distribution, axon density and the myelin g-ratio. AxonSeg includes a simple and intuitive MATLAB-based graphical user interface (GUI) and can easily be adapted to a variety of imaging modalities. The main steps of AxonSeg consist of: (i) image pre-processing; (ii) pre-segmentation of axons over a cropped image and discriminant analysis (DA) to select the best parameters based on axon shape and intensity information; (iii) automatic axon and myelin segmentation over the full image; and (iv) atlas-based statistics to extract morphometric information. Segmentation results from standard optical microscopy (OM), SEM and coherent anti-Stokes Raman scattering (CARS) microscopy are presented, along with validation against manual segmentations. Being fully-automatic after a quick manual intervention on a cropped image, we believe AxonSeg will be useful to researchers interested in large throughput histology. AxonSeg is open source and freely available at: https://github.com/neuropoly/axonseg.
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Affiliation(s)
- Aldo Zaimi
- Institute of Biomedical Engineering, Polytechnique Montreal Montreal, QC, Canada
| | - Tanguy Duval
- Institute of Biomedical Engineering, Polytechnique Montreal Montreal, QC, Canada
| | - Alicja Gasecka
- Institut Universitaire en Santé Mentale de QuébecQuebec, QC, Canada; Centre d'Optique, Photonique et Laser, Université LavalQuebec, QC, Canada
| | - Daniel Côté
- Institut Universitaire en Santé Mentale de QuébecQuebec, QC, Canada; Centre d'Optique, Photonique et Laser, Université LavalQuebec, QC, Canada
| | - Nikola Stikov
- Institute of Biomedical Engineering, Polytechnique MontrealMontreal, QC, Canada; Montreal Heart InstituteMontreal, QC, Canada
| | - Julien Cohen-Adad
- Institute of Biomedical Engineering, Polytechnique MontrealMontreal, QC, Canada; Functional Neuroimaging Unit, CRIUGM, Université de MontréalMontreal, QC, Canada
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Rajagopalan V, Allexandre D, Yue GH, Pioro EP. Diffusion Tensor Imaging Evaluation of Corticospinal Tract Hyperintensity in Upper Motor Neuron-Predominant ALS Patients. J Aging Res 2011; 2011:481745. [PMID: 22132329 PMCID: PMC3205652 DOI: 10.4061/2011/481745] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Accepted: 08/09/2011] [Indexed: 12/03/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) patients with predominant upper motor neuron (UMN) signs occasionally have hyperintensity of corticospinal tract (CST) on T2- and proton-density-(PD-) weighted brain images. Diffusion tensor imaging (DTI) was used to assess whether diffusion parameters along intracranial CST differ in presence or absence of hyperintensity and correspond to UMN dysfunction.
DTI brain scans were acquired in 47 UMN-predominant ALS patients with (n = 21) or without (n = 26) CST hyperintensity and in 10 control subjects. Fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (AD), and radial diffusivity (RD) were measured in four regions of interests (ROIs) along CST. Abnormalities (P < 0.05) were observed in FA, AD, or RD in CST primarily at internal capsule (IC) level in ALS patients, especially those with CST hyperintensity. Clinical measures corresponded well with DTI changes at IC level. The IC abnormalities suggest a prominent axonopathy in UMN-predominant ALS and that tissue changes underlying CST hyperintensity have specific DTI changes, suggestive of unique axonal pathology.
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Affiliation(s)
- Venkateswaran Rajagopalan
- Department of Biomedical Engineering, ND2, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
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Yue S, Slipchenko MN, Cheng JX. Multimodal Nonlinear Optical Microscopy. LASER & PHOTONICS REVIEWS 2011; 5:10.1002/lpor.201000027. [PMID: 24353747 PMCID: PMC3863942 DOI: 10.1002/lpor.201000027] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Accepted: 01/21/2011] [Indexed: 05/17/2023]
Abstract
Because each nonlinear optical (NLO) imaging modality is sensitive to specific molecules or structures, multimodal NLO imaging capitalizes the potential of NLO microscopy for studies of complex biological tissues. The coupling of multiphoton fluorescence, second harmonic generation, and coherent anti-Stokes Raman scattering (CARS) has allowed investigation of a broad range of biological questions concerning lipid metabolism, cancer development, cardiovascular disease, and skin biology. Moreover, recent research shows the great potential of using CARS microscope as a platform to develop more advanced NLO modalities such as electronic-resonance-enhanced four-wave mixing, stimulated Raman scattering, and pump-probe microscopy. This article reviews the various approaches developed for realization of multimodal NLO imaging as well as developments of new NLO modalities on a CARS microscope. Applications to various aspects of biological and biomedical research are discussed.
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Affiliation(s)
- Shuhua Yue
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907
| | - Mikhail N. Slipchenko
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907
| | - Ji-Xin Cheng
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907
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