Quantification of Cervical Cord Cross-Sectional Area: Which Acquisition, Vertebra Level, and Analysis Software? A Multicenter Repeatability Study on a Traveling Healthy Volunteer

EPISeg: Automated segmentation of the spinal cord on echo planar images using open-access multi-center data

Functional magnetic resonance imaging (fMRI) of the spinal cord is relevant for studying sensation, movement, and autonomic function. Preprocessing of spinal cord fMRI data involves segmentation of the spinal cord on gradient-echo echo planar imaging (EPI) images. Current automated segmentation methods do not work well on these data, due to the low spatial resolution, susceptibility artifacts causing distortions and signal drop-out, ghosting, and motion-related artifacts. Consequently, this segmentation task demands a considerable amount of manual effort which takes time and is prone to user bias. In this work, we (i) gathered a multi-center dataset of spinal cord gradient-echo EPI with ground-truth segmentations and shared it on OpenNeuro https://openneuro.org/datasets/ds005143/versions/1.3.0, and (ii) developed a deep learning-based model, EPISeg, for the automatic segmentation of the spinal cord on gradient-echo EPI data. We observe a significant improvement in terms of segmentation quality compared to other available spinal cord segmentation models. Our model is resilient to different acquisition protocols as well as commonly observed artifacts in fMRI data. The training code is available at https://github.com/sct-pipeline/fmri-segmentation/, and the model has been integrated into the Spinal Cord Toolbox as a command-line tool.

Microstructural Damage and Repair in the Spinal Cord of Patients With Early Multiple Sclerosis and Association With Disability at 5 Years

BACKGROUND AND OBJECTIVES

The dynamics of microstructural spinal cord (SC) damage and repair in people with multiple sclerosis (pwMS) and their clinical relevance have yet to be explored. We set out to describe patient-specific profiles of microstructural SC damage and change during the first year after MS diagnosis and to investigate their associations with disability and SC atrophy at 5 years.

METHODS

We performed a longitudinal monocentric cohort study among patients with relapsing-remitting MS: first relapse <1 year, no relapse <1 month, and high initial severity on MRI (>9 T2 lesions on brain MRI and/or initial myelitis). pwMS and age-matched healthy controls (HCs) underwent cervical SC magnetization transfer (MT) imaging at baseline and at 1 year for pwMS. Based on HC data, SC MT ratio z-score maps were computed for each person with MS. An index of microstructural damage was calculated as the proportion of voxels classified as normal at baseline and identified as damaged after 1 year. Similarly, an index of repair was also calculated (voxels classified as damaged at baseline and as normal after 1 year). Linear models including these indices and disability or SC cross-sectional area (CSA) change between baseline and 5 years were implemented.

RESULTS

Thirty-seven patients and 19 HCs were included. We observed considerable variability in the extent of microstructural SC damage at baseline (0%-58% of SC voxels). We also observed considerable variability in damage and repair indices over 1 year (0%-31% and 0%-20%), with 18 patients showing predominance of damage and 18 predominance of repair. The index of microstructural damage was associated positively with the Expanded Disability Status Scale score (r = 0.504, p = 0.002) and negatively with CSA change (r = -0.416, p = 0.02) at 5 years, independent of baseline SC lesion volume.

DISCUSSION

People with early relapsing-remitting MS exhibited heterogeneous profiles of microstructural SC damage and repair. Progression of microstructural damage was associated with disability progression and SC atrophy 5 years later. These results indicate a potential for microstructural repair in the SC to prevent disability progression in pwMS.

Evaluation of cervical spinal cord atrophy using a modified SIENA approach

Spinal cord (SC) atrophy obtained from structural magnetic resonance imaging has gained relevance as an indicator of neurodegeneration in various neurological disorders. The common method to assess SC atrophy is by comparing numerical differences of the cross-sectional spinal cord area (CSA) between time points. However, this indirect approach leads to considerable variability in the obtained results. Studies showed that this limitation can be overcome by using a registration-based technique. The present study introduces the Structural Image Evaluation using Normalization of Atrophy on the Spinal Cord (SIENA-SC), which is an adapted version of the original SIENA method, designed to directly calculate the percentage of SC volume change over time from clinical brain MRI acquired with an extended field of view to cover the superior part of the cervical SC. In this work, we compared SIENA-SC with the Generalized Boundary Shift Integral (GBSI) and the CSA change. On a scan-rescan dataset, SIENA-SC was shown to have the lowest measurement error than the other two methods. When comparing a group of 190 Healthy Controls with a group of 65 Multiple Sclerosis patients, SIENA-SC provided significantly higher yearly rates of atrophy in patients than in controls and a lower sample size when measured for treatment effect sizes of 50%, 30% and 10%. Our findings indicate that SIENA-SC is a robust, reproducible, and sensitive approach for assessing longitudinal changes in spinal cord volume, providing neuroscientists with an accessible and automated tool able to reduce the need for manual intervention and minimize variability in measurements.

Quantifying neurodegeneration of the cervical cord and brain in degenerative cervical myelopathy: A multicentre study using quantitative magnetic resonance imaging

BACKGROUND AND PURPOSE

Simultaneous assessment of neurodegeneration in both the cervical cord and brain across multiple centres can enhance the effectiveness of clinical trials. Thus, this study aims to simultaneously assess microstructural changes in the cervical cord and brain above the stenosis in degenerative cervical myelopathy (DCM) using quantitative magnetic resonance imaging (MRI) in a multicentre study.

METHODS

We applied voxelwise analysis with a probabilistic brain/spinal cord template embedded in statistical parametric mappin (SPM-BSC) to process multi parametric mapping (MPM) including effective transverse relaxation rate (R2*), longitudinal relaxation rate (R1), and magnetization transfer (MT), which are indirectly sensitive to iron and myelin content. Regression analysis was conducted to establish associations between neurodegeneration and clinical impairment. Thirty-eight DCM patients (mean age ± SD = 58.45 ± 11.47 years) and 38 healthy controls (mean age ± SD = 41.18 ± 12.75 years) were recruited at University Hospital Balgrist, Switzerland and Toronto Western Hospital, Canada.

RESULTS

Remote atrophy was observed in the cervical cord (p = 0.002) and in the left thalamus (0.026) of the DCM group. R1 was decreased in the periaqueductal grey matter (p = 0.014), thalamus (p = 0.001), corpus callosum (p = 0.0001), and cranial corticospinal tract (p = 0.03). R2* was increased in the primary somatosensory cortices (p = 0.008). Sensory impairments were associated with increased iron-sensitive R2* in the thalamus and periaqueductal grey matter in DCM.

CONCLUSIONS

Simultaneous assessment of the spinal cord and brain revealed DCM-induced demyelination, iron deposition, and atrophy. The extent of remote neurodegeneration was associated with sensory impairment, highlighting the intricate and expansive nature of microstructural neurodegeneration in DCM, reaching beyond the stenosis level.

Assessing the Equivalence of Brain-Derived Measures from Two 3D T1-Weighted Acquisitions: One Covering the Brain and One Covering the Brain and Spinal Cord

BACKGROUND AND PURPOSE

In MS, it is common to acquire brain and spinal cord MR imaging sequences separately to assess the extent of the disease. The goal of this study was to see how replacing the traditional brain T1-weighted images (brain-T1) with an acquisition that included both the brain and the cervical spinal cord (cns-T1) affected brain- and spinal cord-derived measures.

MATERIALS AND METHODS

Thirty-six healthy controls (HC) and 42 patients with MS were included. Of those, 18 HC and 35 patients with MS had baseline and follow-up at 1 year acquired on a 3T magnet. Two 3D T1-weighted images (brain-T1 and cns-T1) were acquired at each time point. Regional cortical thickness and volumes were determined with FastSurfer, and the percentage brain volume change per year was obtained with SIENA. The spinal cord area was estimated with the Spinal Cord Toolbox. Intraclass correlation coefficients (ICC) were calculated to check for consistency of measures obtained from brain-T1 and cns-T1.

RESULTS

Cortical thickness measures showed an ICC >0.75 in 94% of regions in healthy controls and 80% in patients with MS. Estimated regional volumes had an ICC >0.88, and the percentage brain volume change had an ICC >0.79 for both groups. The spinal cord area measures had an ICC of 0.68 in healthy controls and 0.92 in patients with MS.

CONCLUSIONS

Brain measurements obtained from 3D cns-T1 are highly equivalent to those obtained from a brain-T1, suggesting that it could be feasible to replace the brain-T1 with cns-T1.

Reliability of spinal cord measures based on synthetic T1-weighted MRI derived from multiparametric mapping (MPM)

Short MRI acquisition time, high signal-to-noise ratio, and high reliability are crucial for image quality when scanning healthy volunteers and patients. Cross-sectional cervical cord area (CSA) has been suggested as a marker of neurodegeneration and potential outcome measure in clinical trials and is conventionally measured on T₁-weigthed 3D Magnetization Prepared Rapid Acquisition Gradient-Echo (MPRAGE) images. This study aims to reduce the acquisition time for the comprehensive assessment of the spinal cord, which is typically based on MPRAGE for morphometry and multi-parameter mapping (MPM) for microstructure. The MPRAGE is replaced by a synthetic T₁-w MRI (synT₁-w) estimated from the MPM, in order to measure CSA. SynT₁-w images were reconstructed using the MPRAGE signal equation based on quantitative maps of proton density (PD), longitudinal (R₁) and effective transverse (R₂*) relaxation rates. The reliability of CSA measurements from synT₁-w images was determined within a multi-center test-retest study format and validated against acquired MPRAGE scans by assessing the agreement between both methods. The response to pathological changes was tested by longitudinally measuring spinal cord atrophy following spinal cord injury (SCI) for synT₁-w and MPRAGE using linear mixed effect models. CSA measurements based on the synT₁-w MRI showed high intra-site (Coefficient of variation [CoV]: 1.43% to 2.71%) and inter-site repeatability (CoV: 2.90% to 5.76%), and only a minor deviation of -1.65 mm² compared to MPRAGE. Crucially, by assessing atrophy rates and by comparing SCI patients with healthy controls longitudinally, differences between synT₁-w and MPRAGE were negligible. These results demonstrate that reliable estimates of CSA can be obtained from synT₁-w images, thereby reducing scan time significantly.

Early spinal cord pseudoatrophy in interferon-beta-treated multiple sclerosis

BACKGROUND AND PURPOSE

Brain pseudoatrophy has been shown to play a pivotal role in the interpretation of brain atrophy measures during the first year of disease-modifying therapy in multiple sclerosis. Whether pseudoatrophy also affects the spinal cord remains unclear. The aim of this study was to analyze the extent of pseudoatrophy in the upper spinal cord during the first 2 years after therapy initiation and compare this to the brain.

METHODS

A total of 129 patients from a prospective longitudinal multicentric national cohort study for whom magnetic resonance imaging scans at baseline, 12 months, and 24 months were available were selected for brain and spinal cord volume quantification. Annual percentage brain volume and cord area change were calculated using SIENA (Structural Image Evaluation of Normalized Atrophy) and NeuroQLab, respectively. Linear mixed model analyses were performed to compare patients on interferon-beta therapy (n = 84) and untreated patients (n = 45).

RESULTS

Patients treated with interferon-beta demonstrated accelerated annual percentage brain volume and cervical cord area change in the first year after treatment initiation, whereas atrophy rates stabilized to a similar and not significantly different level compared to untreated patients during the second year.

CONCLUSIONS

These results suggest that pseudoatrophy occurs not only in the brain, but also in the spinal cord during the first year of interferon-beta treatment.

Spinal cord reserve in multiple sclerosis

BACKGROUND

The spinal cord (SC) is a preferential target of multiple sclerosis (MS) damage highly relevant towards disability. Differential impact of such damage could be due to the initial amount of SC tissue, as described for the brain parenchyma (brain reserve concept). We aimed to test the existence of SC reserve by using spinal canal area (SCaA) as a proxy.

METHODS

Brain sagittal three-dimensional T1-weighted scans covering down to C5 level were acquired in 2930 people with MS and 43 healthy controls (HCs) in a cross-sectional, multicentre study. SC area (SCA) and SCaA were obtained with the Spinal Cord Toolbox. Demographical data and patient-derived disability scores were obtained. SC parameters were compared between groups with age-adjusted and sex-adjusted linear regression models. The main outcome of the study, the existence of an association between SCaA and Patient Determined Disease Steps, was tested with scaled linear models.

RESULTS

1747 persons with MS (mean age: 46.35 years; 73.2% female) and 42 HCs (mean age: 45.56 years; 78.6% female) were analysed after exclusion of post-processing errors and application of quality criteria. SCA (60.41 mm² vs 65.02 mm², p<0.001) was lower in people with MS compared with HC; no differences in SCaA were observed (213.24 mm² vs 212.61 mm², p=0.125). Adjusted scaled linear models showed that a larger SCaA was significantly associated with lower scores on Patient Determined Disease Steps (beta coefficient: -0.12, p=0.0124) independently of spinal cord atrophy, brain T2 lesion volume, age and sex.

CONCLUSIONS

A larger SCaA may be protective against disability in MS, possibly supporting the existence of SC reserve.

Reliability of multi-parameter mapping (MPM) in the cervical cord: A multi-center multi-vendor quantitative MRI study

MRI based multicenter studies which target neurological pathologies affecting the spinal cord and brain - including spinal cord injury (SCI) - require standardized acquisition protocols and image processing methods. We have optimized and applied a multi-parameter mapping (MPM) protocol that simultaneously covers the brain and the cervical cord within a traveling heads study across six clinical centers (Leutritz et al., 2020). The MPM protocol includes quantitative maps (magnetization transfer saturation (MT), proton density (PD), longitudinal (R1), and effective transverse (R2*) relaxation rates) sensitive to myelination, water content, iron concentration, and morphometric measures, such as cross-sectional cord area. Previously, we assessed the repeatability and reproducibility of the brain MPM data acquired in the five healthy participants who underwent two scan-rescans (Leutritz et al., 2020). This study focuses on the cervical cord MPM data derived from the same acquisitions to determine its repeatability and reproducibility in the cervical cord. MPM matrices of the cervical cord were generated and processed using the hMRI and the spinal cord toolbox. To determine reliability of the cervical MPM data, the intra-site (i.e., scan-rescan) coefficient of variation (CoV), inter-site CoV, and bias within region of interests (C1, C2 and C3 levels) were determined. The range of the mean intra- and inter-site CoV of MT, R1 and PD was between 2.5% and 12%, and between 1.1% and 4.0% for the morphometric measures. In conclusion, the cervical MPM data showed a high repeatability and reproducibility for key imaging biomarkers and hence can be employed as a standardized tool in multi-center studies, including clinical trials.

Automatic measure and normalization of spinal cord cross-sectional area using the pontomedullary junction

Spinal cord cross-sectional area (CSA) is a relevant biomarker to assess spinal cord atrophy in neurodegenerative diseases. However, the considerable inter-subject variability among healthy participants currently limits its usage. Previous studies explored factors contributing to the variability, yet the normalization models required manual intervention and used vertebral levels as a reference, which is an imprecise prediction of the spinal levels. In this study we implemented a method to measure CSA automatically from a spatial reference based on the central nervous system (the pontomedullary junction, PMJ), we investigated factors to explain variability, and developed normalization strategies on a large cohort (N = 804). Following automatic spinal cord segmentation, vertebral labeling and PMJ labeling, the spinal cord CSA was computed on T1w MRI scans from the UK Biobank database. The CSA was computed using two methods. For the first method, the CSA was computed at the level of the C2-C3 intervertebral disc. For the second method, the CSA was computed at 64 mm caudally from the PMJ, this distance corresponding to the average distance between the PMJ and the C2-C3 disc across all participants. The effect of various demographic and anatomical factors was explored, and a stepwise regression found significant predictors; the coefficients of the best fit model were used to normalize CSA. CSA measured at C2-C3 disc and using the PMJ differed significantly (paired t-test, p-value = 0.0002). The best normalization model included thalamus, brain volume, sex and the interaction between brain volume and sex. The coefficient of variation went down for PMJ CSA from 10.09 (without normalization) to 8.59%, a reduction of 14.85%. For CSA at C2-C3, it went down from 9.96 to 8.42%, a reduction of 15.13 %. This study introduces an end-to-end automatic pipeline to measure and normalize cord CSA from a neurological reference. This approach requires further validation to assess atrophy in longitudinal studies. The inter-subject variability of CSA can be partly accounted for by demographics and anatomical factors.

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.

MAGNIMS recommendations for harmonization of MRI data in MS multicenter studies

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Sharing data from cooperative studies is essential to develop new biomarkers in MS.

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Differences in MRI acquisition, analysis, storage represent a substantial constraint.

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We review the state of the art and developments in the harmonization of MRI.

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We provide recommendations to harmonize large MRI datasets in the MS field.

There is an increasing need of sharing harmonized data from large, cooperative studies as this is essential to develop new diagnostic and prognostic biomarkers. In the field of multiple sclerosis (MS), the issue has become of paramount importance due to the need to translate into the clinical setting some of the most recent MRI achievements. However, differences in MRI acquisition parameters, image analysis and data storage across sites, with their potential bias, represent a substantial constraint. This review focuses on the state of the art, recent technical advances, and desirable future developments of the harmonization of acquisition, analysis and storage of large-scale multicentre MRI data of MS cohorts. Huge efforts are currently being made to achieve all the requirements needed to provide harmonized MRI datasets in the MS field, as proper management of large imaging datasets is one of our greatest opportunities and challenges in the coming years. Recommendations based on these achievements will be provided here. Despite the advances that have been made, the complexity of these tasks requires further research by specialized academical centres, with dedicated technical and human resources. Such collective efforts involving different professional figures are of crucial importance to offer to MS patients a personalised management while minimizing consumption of resources.