Fully automated segmentation of the cervical cord from T1-weighted MRI using PropSeg: Application to multiple sclerosis.

Spinal cord (SC) atrophy, i.e. a reduction in the SC cross-sectional area (CSA) over time, can be measured by means of image segmentation using magnetic resonance imaging (MRI). However, segmentation methods have been limited by factors relating to reproducibility or sensitivity to change. The purpose of this study was to evaluate a fully automated SC segmentation method (PropSeg), and compare this to a semi-automated active surface (AS) method, in healthy controls (HC) and people with multiple sclerosis (MS). MRI data from 120 people were retrospectively analysed; 26 HC, 21 with clinically isolated syndrome, 26 relapsing remitting MS, 26 primary and 21 secondary progressive MS. MRI data from 40 people returning after one year were also analysed. CSA measurements were obtained within the cervical SC. Reproducibility of the measurements was assessed using the intraclass correlation coefficient (ICC). A comparison between mean CSA changes obtained with the two methods over time was performed using multivariate structural equation regression models. Associations between CSA measures and clinical scores were investigated using linear regression models. Compared to the AS method, the reproducibility of CSA measurements obtained with PropSeg was high, both in patients and in HC, with ICC > 0.98 in all cases. There was no significant difference between PropSeg and AS in terms of detecting change over time. Furthermore, PropSeg provided measures that correlated with physical disability, similar to the AS method. PropSeg is a time-efficient and reliable segmentation method, which requires no manual intervention, and may facilitate large multi-centre neuroprotective trials in progressive MS

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

Caractérisation de la microstructure des voies spinales humaines par IRM multiparamétrique

RÉSUMÉ La routine clinique en IRM pour le diagnostic ou le suivi de pathologies neurodégénératives telles que la sclérose en plaques ou la dégénérescence wallérienne ne se fait actuellement que par une évaluation visuelle basée sur des différences de contraste dans des images anatomiques. Il est donc difficile de déterminer précisément le degré des lésions. L’IRM quantitative (IRMq) se propose de quantifier l’évolution du tissu par des métriques sensibles et spécifiques aux différentes caractéristiques microstructurales. Très développé dans le cerveau, sa faisabilité et ses applications ont été démontrées dans la moelle. Toutefois, l’acquisition de telles métriques prend généralement trop de temps et est souvent trop exigeant en termes de force de gradients magnétiques pour entrer dans un cadre clinique. De plus, plusieurs sources d’erreurs sont susceptibles de baiser les mesures. Ce mémoire vise à mettre en place un protocole complet (de l’acquisition au traitement des données) permettant l’estimation de métriques IRMq spécifiquement à chaque voie spinale. Les principales métriques issues de ce protocole sont le Ratio de Transfert de Magnétisation (MTR), le temps de relaxation T1, le Volume de Tissu Macromoléculaire (MTV), les indices des modèles de diffusion NODDI (Neurite Orientation Dispersion and Density Imaging) et DTI (Imagerie par Tenseur de Diffusion), le g-ratio (ratio du diamètre axonal sur celui de la fibre incluant la gaine de myéline) et l’aire de section axiale. Le protocole développé est applicable en clinique et prend en compte les différentes sources d’erreurs connues qui peuvent s’introduire dans les mesures durant l’acquisition. De plus, basé sur le recalage d’un atlas des voies spinales sur chaque métrique, le protocole de traitement de données, rapide et quasi-automatique, permet de s’affranchir du biais lié à l’opérateur lors de la délimitation manuelle des régions d’intérêt. Quant à la méthode d’estimation, elle emploie des estimateurs tels que les estimateurs des moindres carrés et du maximum a posteriori permettant d’atténuer l’effet de volume partiel et du bruit ; elle est par ailleurs validée sur un fantôme synthétique. Finalement, le protocole complet est appliqué à une cohorte de 16 jeunes adultes (de 21 à 33 ans) et 14 adultes âgés (de 61 à 73 ans) sains afin d’évaluer sa sensibilité aux différentes microstructures dans la matière blanche de la moelle épinière. Pour toutes les métriques les estimations montrent des valeurs en accord avec la littérature. Toutes les métriques – excepté les fractions de volume intracellulaire, de volume----------ABSTRACT The current clinical MRI routine for the diagnosis or the screening of neurodegenerative pathologies such as multiple sclerosis or Wallerian degeneration, consists of a simple visual assessment based on contrast differences in anatomical images. Therefore it is hard to precisely assess the stage of the lesions. Quantitative MRI (qMRI) proposes to quantify the evolution of the tissue using metrics sensitive and specific to the different microstructural characteristics. Widely developed in the brain, its feasibility and applications have been demonstrated in the spinal cord. However, the acquisition of such metrics is too time-consuming and demanding in terms of magnetic gradient strength to apply in a clinical framework. Moreover, several sources of error are likely to bias the measures. This thesis aims to develop a comprehensive protocol (from the acquisition to the processing of the data) allowing the estimation of qMRI metrics specifically in each spinal pathway. The main metrics resulting from this protocol are the Magnetization Transfer Ratio (MTR), the relaxation time T1, the Macromolecular Tissue Volume (MTV), the diffusion indices from NODDI (Neurite Orientation Dispersion and Density Imaging) and DTI (Diffusion Tensor Imaging) models, the g-ratio (ratio of the inner diameter over the outer diameter of a fiber, including its myelin sheath) and the cross-sectional area. This protocol is applicable in a clinical framework and takes into account the different sources of error that are likely to affect the measures during acquisition. In addition, since it is based on the registration of a white matter atlas to each metric, the fast and almost automatic data processing pipeline allows to get rid of the usual user-related bias induced by the manual drawing of regions of interest. Moreover, the estimation method uses estimators such as the least square and the maximum a posteriori estimators allowing to mitigate the effect of partial volume and of noise; furthermore, a validation of the method is performed on a synthetic phantom. Finally, the whole protocol is applied to a cohort of 16 young (aged 21 to 33) and 14 elderly (aged 61 to 73) healthy adults in order to assess its sensitivity to different microstructures in the spinal cord white matter. For all metrics the estimations show values in agreement with the literature. All metrics – except the intracellular, the axonal and the fiber volume fractions – showed significant difference between the dorsal column and the corticospinal tract, as suggested by histology. However, only the MTR showed a significant decrease between young and elderly, in agreement wit