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Michael G. Fehlings

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3 papers

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YNIMG Journal 2019 Journal Article

Automatic segmentation of the spinal cord and intramedullary multiple sclerosis lesions with convolutional neural networks

Charley Gros
Benjamin De Leener
Atef Badji
Josefina Maranzano
Dominique Eden
Sara M. Dupont
Jason Talbott
Ren Zhuoquiong

The spinal cord is frequently affected by atrophy and/or lesions in multiple sclerosis (MS) patients. Segmentation of the spinal cord and lesions from MRI data provides measures of damage, which are key criteria for the diagnosis, prognosis, and longitudinal monitoring in MS. Automating this operation eliminates inter-rater variability and increases the efficiency of large-throughput analysis pipelines. Robust and reliable segmentation across multi-site spinal cord data is challenging because of the large variability related to acquisition parameters and image artifacts. In particular, a precise delineation of lesions is hindered by a broad heterogeneity of lesion contrast, size, location, and shape. The goal of this study was to develop a fully-automatic framework — robust to variability in both image parameters and clinical condition — for segmentation of the spinal cord and intramedullary MS lesions from conventional MRI data of MS and non-MS cases. Scans of 1042 subjects (459 healthy controls, 471 MS patients, and 112 with other spinal pathologies) were included in this multi-site study (n = 30). Data spanned three contrasts (T1-, T2-, and T2 ∗-weighted) for a total of 1943 vol and featured large heterogeneity in terms of resolution, orientation, coverage, and clinical conditions. The proposed cord and lesion automatic segmentation approach is based on a sequence of two Convolutional Neural Networks (CNNs). To deal with the very small proportion of spinal cord and/or lesion voxels compared to the rest of the volume, a first CNN with 2D dilated convolutions detects the spinal cord centerline, followed by a second CNN with 3D convolutions that segments the spinal cord and/or lesions. CNNs were trained independently with the Dice loss. When compared against manual segmentation, our CNN-based approach showed a median Dice of 95% vs. 88% for PropSeg (p ≤ 0. 05), a state-of-the-art spinal cord segmentation method. Regarding lesion segmentation on MS data, our framework provided a Dice of 60%, a relative volume difference of −15%, and a lesion-wise detection sensitivity and precision of 83% and 77%, respectively. In this study, we introduce a robust method to segment the spinal cord and intramedullary MS lesions on a variety of MRI contrasts. The proposed framework is open-source and readily available in the Spinal Cord Toolbox.

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YNICL Journal 2016 Journal Article

Translating state-of-the-art spinal cord MRI techniques to clinical use: A systematic review of clinical studies utilizing DTI, MT, MWF, MRS, and fMRI

Allan R. Martin
Izabela Aleksanderek
Julien Cohen-Adad
Zenovia Tarmohamed
Lindsay Tetreault
Nathaniel Smith
David W. Cadotte
Adrian Crawley

BACKGROUND: A recent meeting of international imaging experts sponsored by the International Spinal Research Trust (ISRT) and the Wings for Life Foundation identified 5 state-of-the-art MRI techniques with potential to transform the field of spinal cord imaging by elucidating elements of the microstructure and function: diffusion tensor imaging (DTI), magnetization transfer (MT), myelin water fraction (MWF), MR spectroscopy (MRS), and functional MRI (fMRI). However, the progress toward clinical translation of these techniques has not been established. METHODS: A systematic review of the English literature was conducted using MEDLINE, MEDLINE-in-Progress, Embase, and Cochrane databases to identify all human studies that investigated utility, in terms of diagnosis, correlation with disability, and prediction of outcomes, of these promising techniques in pathologies affecting the spinal cord. Data regarding study design, subject characteristics, MRI methods, clinical measures of impairment, and analysis techniques were extracted and tabulated to identify trends and commonalities. The studies were assessed for risk of bias, and the overall quality of evidence was assessed for each specific finding using the Grading of Recommendations Assessment, Development and Evaluation (GRADE) framework. RESULTS: A total of 6597 unique citations were identified in the database search, and after full-text review of 274 articles, a total of 104 relevant studies were identified for final inclusion (97% from the initial database search). Among these, 69 studies utilized DTI and 25 used MT, with both techniques showing an increased number of publications in recent years. The review also identified 1 MWF study, 11 MRS studies, and 8 fMRI studies. Most of the studies were exploratory in nature, lacking a priori hypotheses and showing a high (72%) or moderately high (20%) risk of bias, due to issues with study design, acquisition techniques, and analysis methods. The acquisitions for each technique varied widely across studies, rendering direct comparisons of metrics invalid. The DTI metric fractional anisotropy (FA) had the strongest evidence of utility, with moderate quality evidence for its use as a biomarker showing correlation with disability in several clinical pathologies, and a low level of evidence that it identifies tissue injury (in terms of group differences) compared with healthy controls. However, insufficient evidence exists to determine its utility as a sensitive and specific diagnostic test or as a tool to predict clinical outcomes. Very low quality evidence suggests that other metrics also show group differences compared with controls, including DTI metrics mean diffusivity (MD) and radial diffusivity (RD), the diffusional kurtosis imaging (DKI) metric mean kurtosis (MK), MT metrics MT ratio (MTR) and MT cerebrospinal fluid ratio (MTCSF), and the MRS metric of N-acetylaspartate (NAA) concentration, although these results were somewhat inconsistent. CONCLUSIONS: State-of-the-art spinal cord MRI techniques are emerging with great potential to improve the diagnosis and management of various spinal pathologies, but the current body of evidence has only showed limited clinical utility to date. Among these imaging tools DTI is the most mature, but further work is necessary to standardize and validate its use before it will be adopted in the clinical realm. Large, well-designed studies with a priori hypotheses, standardized acquisition methods, detailed clinical data collection, and robust automated analysis techniques are needed to fully demonstrate the potential of these rapidly evolving techniques.

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YNIMG Journal 2011 Journal Article

Visualization of cytoplasmic diffusion within living myelin sheaths of CNS white matter axons using microinjection of the fluorescent dye Lucifer Yellow

Alexander A. Velumian
Marina Samoilova
Michael G. Fehlings

The compactness of myelin allows for efficient insulation defining rapid propagation of action potentials, but also raises questions about how cytoplasmic access to its membranes is achieved, which is critical for physiological activity. Understanding the organization of cytoplasmic (‘water’) spaces of myelin is also important for diffusion MRI studies of CNS white matter. Using longitudinal slices of mature rat spinal cord, we monitored the diffusion of the water-soluble fluorescent dye Lucifer Yellow injected into individual oligodendrocytes or internodal myelin. We show that living myelin sheaths on CNS axons are fenestrated by a network of diffusionally interconnected cytoplasmic ‘pockets’ (1. 9±0. 2pockets per 10μm sheath length, n=58) that included Schmidt–Lanterman clefts (SLCs) and numerous smaller compartments. 3-D reconstructions of these cytoplasmic networks show that the outer cytoplasmic layer of CNS myelin is cylindrically ‘encuffing’, which differs from EM studies using fixed tissue. SLCs were found in different ‘open states’ and remained stable within a 1–2hour observation period. Unlike the peripheral nervous system, where similarly small (<500Da) molecules diffuse along the whole myelin segment within a few minutes, in mature CNS this takes more than one hour. The slower cytoplasmic diffusion in CNS myelin possibly contributes to its known vulnerability to injury and limited capacity for repair. Our findings point to an elaborate cytoplasmic access to compact CNS myelin. These results could be of relevance to MRI studies of CNS white matter and to CNS repair/regeneration strategies.

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