A reliable spatially normalized template of the human spinal cord--Applications to automated white matter/gray matter segmentation and tensor-based morphometry (TBM) mapping of gray matter alterations occurring with age

The current state of spinal cord functional magnetic resonance imaging and its application in clinical research

Since its development, spinal cord functional magnetic resonance imaging (fMRI) has utilized various methodologies and stimulation protocols to develop a deeper understanding of a healthy human spinal cord that lays a foundation for its use in clinical research and practice. In this review, we conducted a comprehensive literature search on spinal cord fMRI studies and summarized the recent advancements and resulting scientific achievements of spinal cord fMRI in the following three aspects: the current state of spinal cord fMRI methodologies and stimulation protocols, knowledge about the healthy spinal cord's functions obtained via spinal cord fMRI, and fMRI's exemplary usage in spinal cord diseases and injuries. We conclude with a discussion that, while technical challenges exist, novel fMRI technologies for and new knowledge about the healthy human spinal cord have been established. Empowered by these developments, investigations of pathological and injury states within the spinal cord have become the next important direction of spinal cord fMRI. Recent clinical investigations into spinal cord pathologies, for example, fibromyalgia, multiple sclerosis, spinal cord injury, and cervical spondylotic myelopathy, have already provided deep insights into spinal cord impairments and the time course of impairment-caused changes. We expect that future spinal cord fMRI advancement and research development will further enhance our understanding of various spinal cord diseases and provide the foundation for evaluating existing and developing new treatment plans.

Advanced spinal cord MRI in multiple sclerosis: Current techniques and future directions

Spinal cord magnetic resonance imaging (MRI) has a central role in multiple sclerosis (MS) clinical practice for diagnosis and disease monitoring. Advanced MRI sequences capable of visualizing and quantifying tissue macro- and microstructure and reflecting different pathological disease processes have been used in MS research; however, the spinal cord remains under-explored, partly due to technical obstacles inherent to imaging this structure. We propose that the study of the spinal cord merits equal ambition in overcoming technical challenges, and that there is much information to be exploited to make valuable contributions to our understanding of MS. We present a narrative review on the latest progress in advanced spinal cord MRI in MS, covering in the first part structural, functional, metabolic and vascular imaging methods. We focus on recent studies of MS and those making significant technical steps, noting the challenges that remain to be addressed and what stands to be gained from such advances. Throughout we also refer to other works that presend more in-depth review on specific themes. In the second part, we present several topics that, in our view, hold particular potential. The need for better imaging of gray matter is discussed. We stress the importance of developing imaging beyond the cervical spinal cord, and explore the use of ultra-high field MRI. Finally, some recommendations are given for future research, from study design to newer developments in analysis, and the need for harmonization of sequences and methods within the field. This review is aimed at researchers and clinicians with an interest in gaining an overview of the current state of advanced MRI research in this field and what is primed to be the future of spinal cord imaging in MS research.

Alterations of Brain Networks in Alzheimer's Disease and Mild Cognitive Impairment: A Resting State fMRI Study Based on a Population-specific Brain Template

This study aimed to investigate the alterations in brain networks in patients with Alzheimer's disease (AD) and mild cognitive impairment (MCI) based on a population-specific brain template. Previous studies on AD brain networks using graph theory rarely adopted brain templates specific for certain ethnicities. In this study, patients were divided into 3 groups: AD (n = 24), MCI (n = 27), and healthy controls (HCs, n = 33), and all of the subjects are Chinese. Functional brain networks were constructed for each group based on a Chinese brain template using resting-state functional magnetic resonance imaging (rs-fMRI) data; several graph metrics were calculated. Graph metrics with significant differences after false discovery rate (FDR) correction were analyzed with respect to correlations with four neuropsychological test scores: Mini-Mental State Examination (MMSE), Montreal Cognitive Assessment (MoCA), Activities of Daily Living (ADL), and Clinical Dementia Rating (CDR), which assessed the subjects' cognitive functions and ability to engage in ADL. Graph metrics including assortativity coefficient, nodal degree centrality, nodal clustering coefficient, nodal efficiency, and nodal local efficiency of the frontal gyrus and cerebellum were significantly altered in AD and MCI compared with HC. Several graph metrics were significantly correlated with cognitive function and the ability to engage in daily activities. The findings suggest that altered graph metrics in the frontal gyrus may reflect brain plasticity, and that patients with MCI may have unique graph metric alterations in the cerebellum. Future graph analysis studies on functional brain networks in AD and MCI based on population-specific brain atlases for particular ethnicities may prove valuable.

Sensitivity of the Inhomogeneous Magnetization Transfer Imaging Technique to Spinal Cord Damage in Multiple Sclerosis

BACKGROUND AND PURPOSE

The inhomogeneous magnetization transfer technique has demonstrated high specificity for myelin, and has shown sensitivity to multiple sclerosis-related impairment in brain tissue. Our aim was to investigate its sensitivity to spinal cord impairment in MS relative to more established MR imaging techniques (volumetry, magnetization transfer, DTI).

MATERIALS AND METHODS

Anatomic images covering the cervical spinal cord from the C1 to C6 levels and DTI, magnetization transfer/inhomogeneous magnetization transfer images at the C2/C5 levels were acquired in 19 patients with MS and 19 paired healthy controls. Anatomic images were segmented in spinal cord GM and WM, both manually and using the AMU₄₀ atlases. MS lesions were manually delineated. MR metrics were analyzed within normal-appearing and lesion regions in anterolateral and posterolateral WM and compared using Wilcoxon rank tests and z scores. Correlations between MR metrics and clinical scores in patients with MS were evaluated using the Spearman rank correlation.

RESULTS

AMU₄₀-based C1-to-C6 GM/WM automatic segmentations in patients with MS were evaluated relative to manual delineation. Mean Dice coefficients were 0.75/0.89, respectively. All MR metrics (WM/GM cross-sectional areas, normal-appearing and lesion diffusivities, and magnetization transfer/inhomogeneous magnetization transfer ratios) were observed altered in patients compared with controls (P < .05). Additionally, the absolute inhomogeneous magnetization transfer ratio z scores were significantly higher than those of the other MR metrics (P < .0001), suggesting a higher inhomogeneous magnetization transfer sensitivity toward spinal cord impairment in MS. Significant correlations with the Expanded Disability Status Scale (ρ = -0.73/P = .02, ρ = -0.81/P = .004) and the total Medical Research Council scale (ρ = 0.80/P = .009, ρ = -0.74/P = .02) were observed for inhomogeneous magnetization transfer and magnetization transfer ratio z scores, respectively, in normal-appearing WM regions, while weaker and nonsignificant correlations were obtained for DTI metrics.

CONCLUSIONS

With inhomogeneous magnetization transfer being highly sensitive to spinal cord damage in MS compared with conventional magnetization transfer and DTI, it could generate great clinical interest for longitudinal follow-up and potential remyelinating clinical trials. In line with other advanced myelin techniques with which it could be compared, it opens perspectives for multicentric investigations.

Voxelwise analysis of diffusion MRI of cervical spinal cord using tract-based spatial statistics

Robust voxelwise analysis using tract-based spatial statistics (TBSS) together with permutation statistical method is standardly used in analyzing diffusion tensor imaging (DTI) of brain. A similar analytical method could be useful when studying DTI of cervical spinal cord. Based on anatomical data of sixty-four healthy volunteers, white (WM) and gray matter (GM) masks were created and subsequently registered into DTI space. Using TBSS, two skeleton types were created (single line and dilated for WM as well as GM). From anatomical data, percentage rates of overlap were calculated for all skeletons in relation to WM and GM masks. Voxelwise analysis of fractional anisotropy values depending on age and sex was conducted. Correlation of fraction anisotropy values with age of subjects was also evaluated. The two WM skeleton types showed a high overlap rate with WM masks (~94%); GM skeletons showed lower rates (56% and 42%, respectively, for single line and dilated). WM and GM areas where fraction anisotropy values differ between sexes were identified (p < .05). Furthermore, using voxelwise analysis such WM voxels were identified where fraction anisotropy values differ depending on age (p < .05) and in these voxels linear dependence of fraction anisotropy and age (r = -0.57, p < .001) was confirmed by regression analysis. This dependence was not proven when using WM anatomical masks (r = -0.21, p = .10). The analytical approach presented shown to be useful for group analysis of DTI data for cervical spinal cord.

Regional T1 mapping of the whole cervical spinal cord using an optimized MP2RAGE sequence

The recently-proposed MP2RAGE sequence was purposely optimized for cervical spinal cord imaging at 3T. Sequence parameters were chosen to optimize gray/white matter T₁ contrast with sub-millimetric resolution and scan-time < 10 min while preserving reliable T₁ determination with minimal B₁⁺ variation effects within a range of values compatible with pathologies and surrounding structures. Results showed good agreements with IR-based measurements, high MP2RAGE-based T₁ reproducibility and preliminary evidences of age- and tract-related T₁ variations in the healthy spinal cord.

Spinal Cord Imaging in Amyotrophic Lateral Sclerosis: Historical Concepts-Novel Techniques

Amyotrophic lateral sclerosis (ALS) is the most common adult onset motor neuron disease with no effective disease modifying therapies at present. Spinal cord degeneration is a hallmark feature of ALS, highlighted in the earliest descriptions of the disease by Lockhart Clarke and Jean-Martin Charcot. The anterior horns and corticospinal tracts are invariably affected in ALS, but up to recently it has been notoriously challenging to detect and characterize spinal pathology in vivo. With recent technological advances, spinal imaging now offers unique opportunities to appraise lower motor neuron degeneration, sensory involvement, metabolic alterations, and interneuron pathology in ALS. Quantitative spinal imaging in ALS has now been used in cross-sectional and longitudinal study designs, applied to presymptomatic mutation carriers, and utilized in machine learning applications. Despite its enormous clinical and academic potential, a number of physiological, technological, and methodological challenges limit the routine use of computational spinal imaging in ALS. In this review, we provide a comprehensive overview of emerging spinal cord imaging methods and discuss their advantages, drawbacks, and biomarker potential in clinical applications, clinical trial settings, monitoring, and prognostic roles.

Ten Key Insights into the Use of Spinal Cord fMRI

A comprehensive review of the literature-to-date on functional magnetic resonance imaging (fMRI) of the spinal cord is presented. Spinal fMRI has been shown, over more than two decades of work, to be a reliable tool for detecting neural activity. We discuss 10 key points regarding the history, development, methods, and applications of spinal fMRI. Animal models have served a key purpose for the development of spinal fMRI protocols and for experimental spinal cord injury studies. Applications of spinal fMRI span from animal models across healthy and patient populations in humans using both task-based and resting-state paradigms. The literature also demonstrates clear trends in study design and acquisition methods, as the majority of studies follow a task-based, block design paradigm, and utilize variations of single-shot fast spin-echo imaging methods. We, therefore, discuss the similarities and differences of these to resting-state fMRI and gradient-echo EPI protocols. Although it is newly emerging, complex connectivity and network analysis is not only possible, but has also been shown to be reliable and reproducible in the spinal cord for both task-based and resting-state studies. Despite the technical challenges associated with spinal fMRI, this review identifies reliable solutions that have been developed to overcome these challenges.

Future Brain and Spinal Cord Volumetric Imaging in the Clinic for Monitoring Treatment Response in MS

PURPOSE OF REVIEW

Volumetric analysis of brain imaging has emerged as a standard approach used in clinical research, e.g., in the field of multiple sclerosis (MS), but its application in individual disease course monitoring is still hampered by biological and technical limitations. This review summarizes novel developments in volumetric imaging on the road towards clinical application to eventually monitor treatment response in patients with MS.

RECENT FINDINGS

In addition to the assessment of whole-brain volume changes, recent work was focused on the volumetry of specific compartments and substructures of the central nervous system (CNS) in MS. This included volumetric imaging of the deep brain structures and of the spinal cord white and gray matter. Volume changes of the latter indeed independently correlate with clinical outcome measures especially in progressive MS. Ultrahigh field MRI and quantitative MRI added to this trend by providing a better visualization of small compartments on highly resolving MR images as well as microstructural information. New developments in volumetric imaging have the potential to improve sensitivity as well as specificity in detecting and hence monitoring disease-related CNS volume changes in MS.

Application of Quantitative Microstructural MR Imaging with Atlas-based Analysis for the Spinal Cord in Cervical Spondylotic Myelopathy

Mapping of MR fiber g-ratio, which is the ratio of the diameter of the axon to the diameter of the neuronal fiber, is introduced in this article. We investigated the MR fiber g-ratio, the axon volume fraction (AVF) and the myelin volume fraction (MVF) to evaluate microstructural changes in the spinal cord in patients with cervical spondylotic myelopathy (CSM) in vivo, using atlas-based analysis. We used diffusion MRI data acquired with a new simultaneous multi-slice accelerated readout-segmented echo planar imaging sequence for diffusion analysis for AVF calculation and magnetization transfer saturation imaging for MVF calculation. The AVFs of fasciculus gracilis in the affected side spinal cord, fasciculus cuneatus and lateral corticospinal tracts (LSCT) in the affected and unaffected side spinal cord were significantly lower (P = 0.019, 0.001, 0019, 0.000, and 0.002, respectively) than those of normal controls. No difference was found in the MVFs. The fiber g-ratio of LSCT was significantly lower (P = 0.040) in the affected side spinal cords than in the normal controls. The pathological microstructural changes in the spinal cord in patients with CSM, presumably partial axonal degenerations with preserved myelin. This technique has the potential to be a clinical biomarker in patients with CSM in vivo.

A role for nutritional intervention in addressing the aging neuromuscular junction

The purpose of this review is to discuss the structural and physiological changes that underlie age-related neuromuscular dysfunction and to summarize current evidence on the potential role of nutritional interventions on neuromuscular dysfunction-associated pathways. Age-related neuromuscular deficits are known to coincide with distinct changes in the central and peripheral nervous system, in the neuromuscular system, and systemically. Although many features contribute to the age-related decline in neuromuscular function, a comprehensive understanding of their integration and temporal relationship is needed. Nonetheless, many nutrients and ingredients show promise in modulating neuromuscular output by counteracting the age-related changes that coincide with neuromuscular dysfunction. In particular, dietary supplements, such as vitamin D, omega-3 fatty acids, β-hydroxy-β-methylbutyrate, creatine, and dietary phospholipids, demonstrate potential in ameliorating age-related neuromuscular dysfunction. However, current evidence seldom directly assesses neuromuscular outcomes and is not always in the context of aging. Additional clinical research studies are needed to confirm the benefits of dietary supplements on neuromuscular function, as well as to define the appropriate population, dosage, and duration for intervention.

Region-specific impairment of the cervical spinal cord (SC) in amyotrophic lateral sclerosis: A preliminary study using SC templates and quantitative MRI (diffusion tensor imaging/inhomogeneous magnetization transfer)

In this preliminary study, our objective was to investigate the potential of high-resolution anatomical imaging, diffusion tensor imaging (DTI) and conventional/inhomogeneous magnetization transfer imaging [magnetization transfer (MT)/inhomogeneous magnetization transfer (ihMT)] at 3 T, analyzed with template-extracted regions of interest, to measure the atrophy and structural changes of white (WM) and gray (GM) matter spinal cord (SC) occurring in patients with amyotrophic lateral sclerosis (ALS). Ten patients with ALS and 20 age-matched healthy controls were recruited. SC GM and WM areas were automatically segmented using dedicated templates. Atrophy indices were evaluated from T₂ *-weighted images at each vertebral level from cervical C1 to C6. DTI and ihMT metrics were quantified within the corticospinal tract (CST), posterior sensory tract (PST) and anterior GM (aGM) horns at the C2 and C5 levels. Clinical disabilities of patients with ALS were evaluated using the Revised ALS Functional Rating Scale, upper motor neuron (UMN) and Medical Research Council scorings, and correlated with MR metrics. Compared with healthy controls, GM and WM atrophy was observed in patients with ALS, especially at lower cervical levels, where a strong correlation was also observed between GM atrophy and the UMN score (R = -0.75, p = 0.05 at C6). Interestingly, a significant decrease in ihMT ratio was found in all regions of interest (p < 0.0008), fractional anisotropy (FA) and MT ratios decreased significantly in CST, especially at C5 (p < 0.005), and λ_// (axial diffusivity) decreased significantly in CST (p = 0.0004) and PST (p = 0.003) at C2. Strong correlations between MRI metrics and clinical scores were also found (0.47 < |R| < 0.87, p < 0.05). Altogether, these preliminary results suggest that high-resolution anatomical imaging and ihMT imaging, in addition to DTI, are valuable for the characterization of SC tissue impairment in ALS. In this study, in addition to an important SC WM demyelination, we also observed, for the first time in ALS, impairments of cervical aGM.

Subject-specific regional measures of water diffusion are associated with impairment in chronic spinal cord injury

PURPOSE

We aimed to identify non-invasive imaging parameters that can serve as biomarkers for the integrity of the spinal cord, which is paramount to neurological function. Diffusion tensor imaging (DTI) indices are sensitive to axonal and myelin damage, and have strong potential to serve as such biomarkers. However, averaging DTI indices over large regions of interest (ROIs), a common approach to analyzing the images of injured spinal cord, leads to loss of subject-specific information. We investigated if DTI-tractography-driven, subject-specific demarcation approach can yield measures that are more specific to impairment.

METHODS

In 18 individuals with chronic spinal cord injury (SCI), subject-specific demarcation of the injury region was performed using DTI tractography, which yielded three regions relative to injury (RRI; regions superior to, at, and below injury epicenter). DTI indices averaged over each RRI were correlated with measures of residual motor and sensory function, obtained using the International Standard of Neurological Classification for Spinal Cord Injury (ISNCSCI).

RESULTS

Total ISNCSCI score (ISNCSCI-tot; sum of ISNCSCI motor and sensory scores) was significantly (p < 0.05) correlated with fractional anisotropy and axial and radial diffusivities. ISNCSCI-tot showed strongest correlation with indices measured from the region inferior to the injury epicenter (IRRI), the degree of which exceeded that of those measured from the entire cervical cord-suggesting contribution from Wallerian degeneration.

CONCLUSION

DTI tractography-driven, subject-specific injury demarcation approach provided measures that were more specific to impairment. Notably, DTI indices obtained from the IRRI region showed the highest specificity to impairment, demonstrating their strong potential as biomarkers for the SCI severity.

Spinal cord grey matter segmentation challenge

An important image processing step in spinal cord magnetic resonance imaging is the ability to reliably and accurately segment grey and white matter for tissue specific analysis. There are several semi- or fully-automated segmentation methods for cervical cord cross-sectional area measurement with an excellent performance close or equal to the manual segmentation. However, grey matter segmentation is still challenging due to small cross-sectional size and shape, and active research is being conducted by several groups around the world in this field. Therefore a grey matter spinal cord segmentation challenge was organised to test different capabilities of various methods using the same multi-centre and multi-vendor dataset acquired with distinct 3D gradient-echo sequences. This challenge aimed to characterize the state-of-the-art in the field as well as identifying new opportunities for future improvements. Six different spinal cord grey matter segmentation methods developed independently by various research groups across the world and their performance were compared to manual segmentation outcomes, the present gold-standard. All algorithms provided good overall results for detecting the grey matter butterfly, albeit with variable performance in certain quality-of-segmentation metrics. The data have been made publicly available and the challenge web site remains open to new submissions. No modifications were introduced to any of the presented methods as a result of this challenge for the purposes of this publication.

Topologically preserving straightening of spinal cord MRI

PURPOSE

To propose a robust and accurate method for straightening magnetic resonance (MR) images of the spinal cord, based on spinal cord segmentation, that preserves spinal cord topology and that works for any MRI contrast, in a context of spinal cord template-based analysis.

MATERIALS AND METHODS

The spinal cord curvature was computed using an iterative Non-Uniform Rational B-Spline (NURBS) approximation. Forward and inverse deformation fields for straightening were computed by solving analytically the straightening equations for each image voxel. Computational speed-up was accomplished by solving all voxel equation systems as one single system. Straightening accuracy (mean and maximum distance from straight line), computational time, and robustness to spinal cord length was evaluated using the proposed and the standard straightening method (label-based spline deformation) on 3T T₂ - and T₁ -weighted images from 57 healthy subjects and 33 patients with spinal cord compression due to degenerative cervical myelopathy (DCM).

RESULTS

The proposed algorithm was more accurate, more robust, and faster than the standard method (mean distance = 0.80 vs. 0.83 mm, maximum distance = 1.49 vs. 1.78 mm, time = 71 vs. 174 sec for the healthy population and mean distance = 0.65 vs. 0.68 mm, maximum distance = 1.28 vs. 1.55 mm, time = 32 vs. 60 sec for the DCM population).

CONCLUSION

A novel image straightening method that enables template-based analysis of quantitative spinal cord MRI data is introduced. This algorithm works for any MRI contrast and was validated on healthy and patient populations. The presented method is implemented in the Spinal Cord Toolbox, an open-source software for processing spinal cord MRI data.

LEVEL OF EVIDENCE

1 Technical Efficacy: Stage 1 J. Magn. Reson. Imaging 2017;46:1209-1219.

SCT: Spinal Cord Toolbox, an open-source software for processing spinal cord MRI data

For the past 25 years, the field of neuroimaging has witnessed the development of several software packages for processing multi-parametric magnetic resonance imaging (mpMRI) to study the brain. These software packages are now routinely used by researchers and clinicians, and have contributed to important breakthroughs for the understanding of brain anatomy and function. However, no software package exists to process mpMRI data of the spinal cord. Despite the numerous clinical needs for such advanced mpMRI protocols (multiple sclerosis, spinal cord injury, cervical spondylotic myelopathy, etc.), researchers have been developing specific tools that, while necessary, do not provide an integrative framework that is compatible with most usages and that is capable of reaching the community at large. This hinders cross-validation and the possibility to perform multi-center studies. In this study we introduce the Spinal Cord Toolbox (SCT), a comprehensive software dedicated to the processing of spinal cord MRI data. SCT builds on previously-validated methods and includes state-of-the-art MRI templates and atlases of the spinal cord, algorithms to segment and register new data to the templates, and motion correction methods for diffusion and functional time series. SCT is tailored towards standardization and automation of the processing pipeline, versatility, modularity, and it follows guidelines of software development and distribution. Preliminary applications of SCT cover a variety of studies, from cross-sectional area measures in large databases of patients, to the precise quantification of mpMRI metrics in specific spinal pathways. We anticipate that SCT will bring together the spinal cord neuroimaging community by establishing standard templates and analysis procedures.

Fully-integrated framework for the segmentation and registration of the spinal cord white and gray matter

The spinal cord white and gray matter can be affected by various pathologies such as multiple sclerosis, amyotrophic lateral sclerosis or trauma. Being able to precisely segment the white and gray matter could help with MR image analysis and hence be useful in further understanding these pathologies, and helping with diagnosis/prognosis and drug development. Up to date, white/gray matter segmentation has mostly been done manually, which is time consuming, induces a bias related to the rater and prevents large-scale multi-center studies. Recently, few methods have been proposed to automatically segment the spinal cord white and gray matter. However, no single method exists that combines the following criteria: (i) fully automatic, (ii) works on various MRI contrasts, (iii) robust towards pathology and (iv) freely available and open source. In this study we propose a multi-atlas based method for the segmentation of the spinal cord white and gray matter that addresses the previous limitations. Moreover, to study the spinal cord morphology, atlas-based approaches are increasingly used. These approaches rely on the registration of a spinal cord template to an MR image, however the registration usually doesn't take into account the spinal cord internal structure and thus lacks accuracy. In this study, we propose a new template registration framework that integrates the white and gray matter segmentation to account for the specific gray matter shape of each individual subject. Validation of segmentation was performed in 24 healthy subjects using T₂^*-weighted images, in 8 healthy subjects using diffusion weighted images (exhibiting inverted white-to-gray matter contrast compared to T₂*-weighted), and in 5 patients with spinal cord injury. The template registration was validated in 24 subjects using T₂*-weighted data. Results of automatic segmentation on T₂*-weighted images was in close correspondence with the manual segmentation (Dice coefficient in the white/gray matter of 0.91/0.71 respectively). Similarly, good results were obtained in data with inverted contrast (diffusion-weighted image) and in patients. When compared to the classical template registration framework, the proposed framework that accounts for gray matter shape significantly improved the quality of the registration (comparing Dice coefficient in gray matter: p=9.5×10^-6). While further validation is needed to show the benefits of the new registration framework in large cohorts and in a variety of patients, this study provides a fully-integrated tool for quantitative assessment of white/gray matter morphometry and template-based analysis. All the proposed methods are implemented in the Spinal Cord Toolbox (SCT), an open-source software for processing spinal cord multi-parametric MRI data.

Gray matter segmentation of the spinal cord with active contours in MR images

OBJECTIVE

Fully or partially automated spinal cord gray matter segmentation techniques for spinal cord gray matter segmentation will allow for pivotal spinal cord gray matter measurements in the study of various neurological disorders. The objective of this work was multi-fold: (1) to develop a gray matter segmentation technique that uses registration methods with an existing delineation of the cord edge along with Morphological Geodesic Active Contour (MGAC) models; (2) to assess the accuracy and reproducibility of the newly developed technique on 2D PSIR T1 weighted images; (3) to test how the algorithm performs on different resolutions and other contrasts; (4) to demonstrate how the algorithm can be extended to 3D scans; and (5) to show the clinical potential for multiple sclerosis patients.

METHODS

The MGAC algorithm was developed using a publicly available implementation of a morphological geodesic active contour model and the spinal cord segmentation tool of the software Jim (Xinapse Systems) for initial estimate of the cord boundary. The MGAC algorithm was demonstrated on 2D PSIR images of the C2/C3 level with two different resolutions, 2D T2* weighted images of the C2/C3 level, and a 3D PSIR image. These images were acquired from 45 healthy controls and 58 multiple sclerosis patients selected for the absence of evident lesions at the C2/C3 level. Accuracy was assessed though visual assessment, Hausdorff distances, and Dice similarity coefficients. Reproducibility was assessed through interclass correlation coefficients. Validity was assessed through comparison of segmented gray matter areas in images with different resolution for both manual and MGAC segmentations.

RESULTS

Between MGAC and manual segmentations in healthy controls, the mean Dice similarity coefficient was 0.88 (0.82-0.93) and the mean Hausdorff distance was 0.61 (0.46-0.76) mm. The interclass correlation coefficient from test and retest scans of healthy controls was 0.88. The percent change between the manual segmentations from high and low-resolution images was 25%, while the percent change between the MGAC segmentations from high and low resolution images was 13%. Between MGAC and manual segmentations in MS patients, the average Dice similarity coefficient was 0.86 (0.8-0.92) and the average Hausdorff distance was 0.83 (0.29-1.37) mm.

CONCLUSION

We demonstrate that an automatic segmentation technique, based on a morphometric geodesic active contours algorithm, can provide accurate and precise spinal cord gray matter segmentations on 2D PSIR images. We have also shown how this automated technique can potentially be extended to other imaging protocols.

Tract-specific and age-related variations of the spinal cord microstructure: a multi-parametric MRI study using diffusion tensor imaging (DTI) and inhomogeneous magnetization transfer (ihMT)

Being able to finely characterize the spinal cord (SC) microstructure and its alterations is a key point when investigating neural damage mechanisms encountered in different central nervous system (CNS) pathologies, such as multiple sclerosis, amyotrophic lateral sclerosis or myelopathy. Based on novel methods, including inhomogeneous magnetization transfer (ihMT) and dedicated SC probabilistic atlas post-processing, the present study focuses on the in vivo characterization of the healthy SC tissue in terms of regional microstructure differences between (i) upper and lower cervical vertebral levels and (ii) sensory and motor tracts, as well as differences attributed to normal aging. Forty-eight healthy volunteers aged from 20 to 70 years old were included in the study and scanned at 3 T using axial high-resolution T2 *-w imaging, diffusion tensor imaging (DTI) and ihMT, at two vertebral levels (C2 and C5). A processing pipeline with minimal user intervention, SC segmentation and spatial normalization into a reference space was implemented in order to assess quantitative morphological and structural parameters (cross-sectional areas, scalar DTI and MT/ihMT metrics) in specific white and gray matter regions of interest. The multi-parametric MRI metrics collected allowed upper and lower cervical levels to be distinguished, with higher ihMT ratio (ihMTR), higher axial diffusivity (λ∥ ) and lower radial diffusivity (λ⊥ ) at C2 compared with C5. Significant differences were also observed between white matter fascicles, with higher ihMTR and lower λ∥ in motor tracts compared with posterior sensory tracts. Finally, aging was found to be associated with significant metric alterations (decreased ihMTR and λ∥ ). The methodology proposed here, which can be easily transferred to the clinic, provides new insights for SC characterization. It bears great potential to study focal and diffuse SC damage in neurodegenerative and demyelinating diseases. Copyright © 2016 John Wiley & Sons, Ltd.

Cervical Spinal Cord Atrophy Profile in Adult SMN1-Linked SMA

PURPOSE

The mechanisms underlying the topography of motor deficits in spinal muscular atrophy (SMA) remain unknown. We investigated the profile of spinal cord atrophy (SCA) in SMN1-linked SMA, and its correlation with the topography of muscle weakness.

MATERIALS AND METHODS

Eighteen SMN1-linked SMA patients type III/V and 18 age/gender-matched healthy volunteers were included. Patients were scored on manual muscle testing and functional scales. Spinal cord was imaged using 3T MRI system. Radial distance (RD) and cord cross-sectional area (CSA) measurements in SMA patients were compared to those in controls and correlated with strength and disability scores.

RESULTS

CSA measurements revealed a significant cord atrophy gradient mainly located between C3 and C6 vertebral levels with a SCA rate ranging from 5.4% to 23% in SMA patients compared to controls. RD was significantly lower in SMA patients compared to controls in the anterior-posterior direction with a maximum along C4 and C5 vertebral levels (p-values < 10-5). There were no correlations between atrophy measurements, strength and disability scores.

CONCLUSIONS

Spinal cord atrophy in adult SMN1-linked SMA predominates in the segments innervating the proximal muscles. Additional factors such as neuromuscular junction or intrinsic skeletal muscle defects may play a role in more complex mechanisms underlying weakness in these patients.

Magnetization transfer from inhomogeneously broadened lines (ihMT): Improved imaging strategy for spinal cord applications

PURPOSE

Inhomogeneous magnetization transfer (ihMT) shows great promise for specific imaging of myelinated tissues. Whereas the ihMT technique has been previously applied in brain applications, the current report presents a strategy for cervical spinal cord (SC) imaging free of cerebrospinal fluid (CSF) pulsatility artifacts.

METHODS

A pulsed ihMT preparation was combined with a single-shot HASTE readout. Electrocardiogram (ECG) synchronization was used to acquire all images during the quiescent phase of SC motion. However ihMT signal quantification errors may occur when a variable recovery delay is introduced in the sequence as a consequence of variable cardiac cycle. A semiautomatic retrospective correction algorithm, based on repetition time (TR) -matching, is proposed to correct for signal variations of long T₁ -components (e.g., CSF).

RESULTS

The proposed strategy combining ECG synchronization and retrospective data pairing led to clean SC images free of CSF artifacts. Lower variability of the ihMT metrics were obtained with the correction algorithm, and allowed for shorter TR to be used, hence improving signal-to-noise ratio efficiency.

CONCLUSION

The proposed methodology enabled faster acquisitions, while offering robust ihMT quantification and exquisite SC image quality. This opens great perspectives for widening the in vivo characterization of SC physiopathology using MRI, such as studying white matter tracts microstructure or impairment in degenerative pathologies. Magn Reson Med 77:581-591, 2017. © 2016 International Society for Magnetic Resonance in Medicine.

Segmentation of the human spinal cord

Segmenting the spinal cord contour is a necessary step for quantifying spinal cord atrophy in various diseases. Delineating gray matter (GM) and white matter (WM) is also useful for quantifying GM atrophy or for extracting multiparametric MRI metrics into specific WM tracts. Spinal cord segmentation in clinical research is not as developed as brain segmentation, however with the substantial improvement of MR sequences adapted to spinal cord MR investigations, the field of spinal cord MR segmentation has advanced greatly within the last decade. Segmentation techniques with variable accuracy and degree of complexity have been developed and reported in the literature. In this paper, we review some of the existing methods for cord and WM/GM segmentation, including intensity-based, surface-based, and image-based methods. We also provide recommendations for validating spinal cord segmentation techniques, as it is important to understand the intrinsic characteristics of the methods and to evaluate their performance and limitations. Lastly, we illustrate some applications in the healthy and pathological spinal cord. One conclusion of this review is that robust and automatic segmentation is clinically relevant, as it would allow for longitudinal and group studies free from user bias as well as reproducible multicentric studies in large populations, thereby helping to further our understanding of the spinal cord pathophysiology and to develop new criteria for early detection of subclinical evolution for prognosis prediction and for patient management. Another conclusion is that at the present time, no single method adequately segments the cord and its substructure in all the cases encountered (abnormal intensities, loss of contrast, deformation of the cord, etc.). A combination of different approaches is thus advised for future developments, along with the introduction of probabilistic shape models. Maturation of standardized frameworks, multiplatform availability, inclusion in large suite and data sharing would also ultimately benefit to the community.

White matter atlas of the human spinal cord with estimation of partial volume effect

Template-based analysis has proven to be an efficient, objective and reproducible way of extracting relevant information from multi-parametric MRI data. Using common atlases, it is possible to quantify MRI metrics within specific regions without the need for manual segmentation. This method is therefore free from user-bias and amenable to group studies. While template-based analysis is common procedure for the brain, there is currently no atlas of the white matter (WM) spinal pathways. The goals of this study were: (i) to create an atlas of the white matter tracts compatible with the MNI-Poly-AMU template and (ii) to propose methods to quantify metrics within the atlas that account for partial volume effect. The WM atlas was generated by: (i) digitalizing an existing WM atlas from a well-known source (Gray's Anatomy), (ii) registering this atlas to the MNI-Poly-AMU template at the corresponding slice (C4 vertebral level), (iii) propagating the atlas throughout all slices of the template (C1 to T6) using regularized diffeomorphic transformations and (iv) computing partial volume values for each voxel and each tract. Several approaches were implemented and validated to quantify metrics within the atlas, including weighted-average and Gaussian mixture models. Proof-of-concept application was done in five subjects for quantifying magnetization transfer ratio (MTR) in each tract of the atlas. The resulting WM atlas showed consistent topological organization and smooth transitions along the rostro-caudal axis. The median MTR across tracts was 26.2. Significant differences were detected across tracts, vertebral levels and subjects, but not across laterality (right-left). Among the different tested approaches to extract metrics, the maximum a posteriori showed highest performance with respect to noise, inter-tract variability, tract size and partial volume effect. This new WM atlas of the human spinal cord overcomes the biases associated with manual delineation and partial volume effect. Combined with multi-parametric data, the atlas can be applied to study demyelination and degeneration in diseases such as multiple sclerosis and will facilitate the conduction of longitudinal and multi-center studies.