Segmentation of Multiple Sclerosis Lesions across Hospitals: Learn Continually or Train from Scratch?

Segmentation of Multiple Sclerosis (MS) lesions is a challenging problem. Several deep-learning-based methods have been proposed in recent years. However, most methods tend to be static, that is, a single model trained on a large, specialized dataset, which does not generalize well. Instead, the model should learn across datasets arriving sequentially from different hospitals by building upon the characteristics of lesions in a continual manner. In this regard, we explore experience replay, a well-known continual learning method, in the context of MS lesion segmentation across multi-contrast data from 8 different hospitals. Our experiments show that replay is able to achieve positive backward transfer and reduce catastrophic forgetting compared to sequential fine-tuning. Furthermore, replay outperforms the multi-domain training, thereby emerging as a promising solution for the segmentation of MS lesions. The code is available at this link: https://github.com/naga-karthik/continual-learning-msComment: Accepted at the Medical Imaging Meets NeurIPS (MedNeurIPS) Workshop 202

Encapsulation et vectorisation de l'hélium3 hyperpolarisé (application à l'IRM de la perfusion tissulaire)

L'émergence des gaz hyperpolarisés (129Xe, 3He) dans le domaine de l'Imagerie par Résonance Magnétique Nucléaire a créé de nouvelles opportunités pour l'imagerie médicale, telles que l'imagerie de la ventilation pulmonaire et l'imagerie de la perfusion tissulaire. Ce manuscrit est consacré aux premiers travaux réalisés en imagerie de perfusion avec l'hélium3 hyperpolarisé. L'hélium3, polarisé par pompage optique (méthode directe) à l'institut Laûe-Langevin (Grenoble), est un gaz de faible solubilité dans le sang, il ne peut donc pas être utilisé après inhalation pour des études intavasculaires. Pour autoriser son utilisation dans le système sanguin, nous avons donc élaboré, en collaboration avec la société Bracco-Research (Genève), une méthode de vectorisation : l'hélium se trouve encapsulé dans des microbulles constituées de phospholipides. Le diamètre moyen de ces micobulles est de 3 micros m, c'est à dire inférieur à la taille des capillaires, les microbulles peuvent être donc injectées sans risque d'obstruction. Les paramètres RMN de l'hélium encapsulé ont été mesurés et s'avèrent suffisamment bien adaptés pour permettre le passage à l'imagerie. L'objet de cette thèse est l'utilusation de l'hélium encapsulé pour des applications de perfusion tissulaire. Le premier chapitre rappelle les principes généraux de la RMN et réprésente les gaz hyperpolarisés ainsi que leur emploi en IRM. Le deuxième chapitre est consacré à la détermination des caractéristiques des microbulles et à la mesure des paramètres physiques de l'hélium encapsulé. le troisième chapitre est dédié au développement de l'imagerie de la perfusion pulmùnaire avec l'hélium encapsulé et le quatrième à l'imagerie des coronaires et à l'imagerie de la perfusion du myocarde. Ces chapitres démontrent, les potentialités de l'hélium encapsulé pour l'étude de la perfusion tissulaire. Le dernier chapitre est enfin consacré à la quantification de la perfusion à partir des données iconographiques obtenues avec l'hélium.LYON1-BU.Sciences (692662101) / SudocSudocFranceF

In vivo mouse spinal cord imaging using echo-planar imaging at 11.75 T

Object To evaluate the feasibility of mouse spinal cord MR imaging using echo-planar imaging (EPI). Materials and methods Optimized multi-shot spin-echo-EPI sequences were compared to conventional spin-echo (c-SE) at 11.75 T and used for high-spatially resolved acquisitions and relaxation-time measurements. Results Good quality images were obtained, with clear delineation of gray and white matter. Acquisition-time gain factor was up to 6 (vs. c-SE) and resolution up to 74 × 94 μm(2) was achieved. T(1) and T(2) relaxation times were reliably measured. Conclusion High-temporally and spatially resolved mouse spinal cord EPI imaging is feasible. This technique should greatly benefit to long acquisition-time experiments (diffusion imaging) and imaging of rapidly-evolving pathologies

Anterior fissure, central canal, posterior septum and more: New insights into the cervical spinal cord gray and white matter regional organization using T1 mapping at 7T

International audienceT1 mapping lacks specificity toward a single particular biological feature, however it has the potential to discriminate spinal cord regional tissue organization and characterize tissue microstructural impairments occurring in neurodegenerative pathologies. In this exploratory work, T1 mapping of the cervical spinal cord with a 300-μm in-plane resolution was performed on fourteen healthy subjects at 7T, using the MP2RAGE sequence. Individual images from C1 to C7 vertebral levels provided a clear delineation of spinal cord anatomical details and substructures including motor columns within gray matter (GM) horns, anterior median fissure, central canal, ventral, lateral and dorsal white matter (WM) fasciculi, and posterior median septum. Group studies highlighted regional T1 differences between regions of interest so far hardly visible at lower spatial resolution. Two-dimensional averaged T1 maps and manual parcellation of GM and WM substructures were built based on these data. Benefiting from the very high spatial resolution achievable at ultra-high field for T1 mapping, this work contributes to improve the in vivo characterization of the cervical spinal cord. By allowing investigation within a wider range of functional regions, it also opens new perspectives for pathology diagnosis such as motor neuron disease, neuropathic pain or refined investigation of neurodegeneration

Spinal cord blood flow measurement by arterial spin labeling

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Cervical Canal Morphology: Effects of Neck Flexion in Normal Condition - New Elements for Biomechanical Simulations and Surgical Management

Continuous measurements and computation of absolute metrics of cervical subarachnoid space (CSS) and spinal cord (SC) geometries proposed are based on in vivo magnetic resonance imaging and 3D reconstruction. OBJECTIVE: The aim of the study is to offer a new methodology to continuously characterize and to quantify the detailed morphology of the CSS and the cervical SC in 3D for healthy subjects in both neutral supine and flexion. SUMMARY OF BACKGROUND DATA: To the best of our knowledge, no study provide a morphological quantification by absolute indices based on the 3D reconstruction of SC and CSS thanks to in vivo magnetic resonance imaging. Moreover, no study provide a continuous description of the geometries. METHODS: Absolute indices of SC (cross-sectional area, compression ratio, position in the canal, length) and of CSS (cross-sectional area, occupational ratio, lengths) were computed by measures from 3D semi-automatic reconstructions of high resolution in vivo magnetic resonance images (3D T2-SPACE sequence) on healthy subjects (N=11) for two postures: supine neutral and flexion neck positions. The variability induced by the semi-automatic reconstruction and by the landmarks positioning were investigated by preliminary sensitivity analyses. Inter and intra-variability were also quantified on a randomly chosen part of our population (N = 5). RESULTS: The length and cross-sectional area of SC are significantly different (p \textless 0.05) in flexion compared to neutral neck position. Spinal cord stays centered in the canal for both postures. However, the cross-sectional area of CSS is submitted to low variation after C3 vertebra for both postures. OR and CR after C3 are significantly lower in flexion. CONCLUSIONS: This study presented interpretations of morphological measures: 1) left-right stability (described by the Left-Right eccentricity index) ensured by the denticulate ligaments and the nerve roots attached to the dural sheaths, 2) a Poisson effect of the SC was partially notified through its axial (AP diameter, OR, CR) and its longitudinal geometrical descriptions (LSC). Such morphological data can be useful for geometrical finite element modeling and could now be used to compare with injured or symptomatic subjects

Geometrical variations in white and gray matter affect the biomechanics of spinal cord injuries more than the arachnoid space

Traumatic spinal cord contusions lead to loss of quality of life, but their pathomechanisms are not fully understood. Previous studies have underlined the contribution of the cerebrospinal fluid in spinal cord protection. However, it remains unclear how important the contribution of the cerebrospinal fluid is relative to other factors such as the white/gray matter ratio. A finite element model of the spinal cord and surrounding morphologic features was used to investigate the spinal cord contusion mechanisms, considering subarachnoid space and white/gray matter ratio. Two vertebral segments (T6 and L1) were impacted transversely at 4.5ms-1, which demonstrated three major results: While the presence of cerebrospinal fluid plays a significant contributory role in spinal cord protection (compression percentage decreased by up to 19%), the arachnoid space variation along the spine appears to have a limited (3% compression decrease) impact; Differences in the white and gray matter geometries from lumbar to thoracic spine levels decrease spinal cord compression by up to 14% at the thoracic level ; Stress distribution in the sagittal spinal cord section was consistent with central cord syndrome, and local stress concentration on the anterior part of the spinal cord being highly reduced by the presence of cerebrospinal fluid. The use of a refined spinal cord finite element method showed that all the geometrical parameters are involved in the spinal cord contusion mechanisms. Hence, spinal cord injury criteria must be considered at each vertebral level

Short-scan-time multi-slice diffusion MRI of the mouse cervical spinal cord using echo planar imaging

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Feasibility of human spinal cord perfusion mapping using dynamic susceptibility contrast imaging at 7T: Preliminary results and identified guidelines

International audiencePurposeTo explore the feasibility of dynamic susceptibility contrast MRI at 7 Tesla for human spinal cord perfusion mapping and fill the gap between brain and spinal cord perfusion mapping techniques.MethodsAcquisition protocols for high‐resolution single shot EPI in the spinal cord were optimized for both spin‐echo and gradient‐echo preparations, including cardiac gating, acquisition times and breathing cycle recording. Breathing‐induced MRI signal fluctuations were investigated in healthy volunteers. A specific image‐ and signal‐processing pipeline was implemented to address them. Dynamic susceptibility contrast was then evaluated in 3 healthy volunteers and 5 patients. Bolus depiction on slice‐wise signal within cord was investigated, and maps of relative perfusion indices were computed.ResultsSignal fluctuations were increased by 1.9 and 2.3 in free‐breathing compared to apnea with spin‐echo and gradient‐echo, respectively. The ratio between signal fluctuations and bolus peak in healthy volunteers was 5.0% for spin‐echo and 3.8% for gradient‐echo, allowing clear depiction of the bolus on every slice and yielding relative blood flow and volume maps exhibiting the expected higher perfusion of gray matter. However, signal fluctuations in patients were increased by 4 in average (using spin‐echo), compromising the depiction of the bolus in slice‐wise signal. Moreover, 3 of 18 slices had to be discarded because of fat‐aliasing artifacts.ConclusionDynamic susceptibility contrast MRI at 7 Tesla showed great potential for spinal cord perfusion mapping with a reliability never achieved thus far for single subject and single slice measurements. Signal stability needs to be improved in acquisition conditions associated with patients; guidelines to achieve that have been identified and shared