Benjamin De Leener

• Ph.D.
• Professor (Assistant) at Polytechnique Montréal

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 brai...

Spinal cord segmentation provides measures of atrophy and facilitates group analysis via inter-subject correspondence. Automatizing this procedure enables studies with large throughput and minimizes user bias. Although several automatic segmentation methods exist, they are often restricted in terms of image contrast and field-of-view. This paper pr...

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...

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 manu...

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...

Purpose Lumbar paraspinal intramuscular fat (IMF) has emerged as a biological factor in low back pain (LBP). Traditional assessments measure IMF across the entire muscle or at specific levels and may miss key information on the role of IMF in LBP. Despite known variations across the lumbar spine, the three-dimensional (3D) distribution of IMF has n...

Somatotopy, the topographical arrangement of sensorimotor pathways corresponding to distinct body parts, is a fundamental feature of the human central nervous system (CNS). Traditionally, investigations into brain and spinal cord somatotopy have been conducted independently, primarily utilizing body stimulations or movements. To date, however, no s...

Clinical research emphasizes the implementation of rigorous and reproducible study designs that rely on between-group matching or controlling for sources of biological variation such as subject’s sex and age. However, corrections for body size (i.e. height and weight) are mostly lacking in clinical neuroimaging designs. This study investigates the...

Somatotopy, the topographical arrangement of sensorimotor pathways corresponding to distinct body parts, is a fundamental feature of the human central nervous system (CNS). Traditionally, investigations into brain and spinal cord somatotopy have been conducted independently, primarily utilizing body stimulations or movements. To date, however, no s...

OHBM Brainhack 2022 took place in June 2022. The first hybrid OHBM hackathon, it had an in-person component taking place in Glasgow and three hubs around the globe to improve inclusivity and fit as many timezones as possible. In the buzzing setting of the Queen Margaret Union and of the virtual platform, 23 projects were presented after development...

Simultaneous functional magnetic resonance imaging (fMRI) of the spinal cord and brain represents a powerful method for examining both ascending sensory and descending motor pathways in humans in vivo . However, its image acquisition protocols, and processing pipeline are less well established. This limitation is mainly due to technical difficultie...

The spinal cord is a critical component of the central nervous system, transmitting and integrating signals between the brain and the periphery via topographically organized functional levels. Despite its central role in sensorimotor processes and several neuromotor disorders, mapping the functional organization of the spinal cord in vivo in humans...

Introduction Chronic progressive neuroinflammation is a hallmark of neurological lysosomal storage diseases, including mucopolysaccharidosis III (MPS III or Sanfilippo disease). Since neuroinflammation is linked to white matter tract pathology, we analyzed axonal myelination and white matter density in the mouse model of MPS IIIC HgsnatP304L and po...

Background: Parkinson's disease (PD) has traditionally been viewed as an α-synucleinopathy brain pathology. Yet evidence based on postmortem human and animal experimental models indicates that the spinal cord may also be affected. Objective: Functional magnetic resonance imaging (fMRI) seems to be a promising candidate to better characterize spi...

Segmentation of the spinal cord is an essential process for the accurate delineation of spinal cord structures but can be a tedious task for experts when using manual or semi‐automated tools. On the other hand, existing automatic segmentation algorithms have not been developed with the pediatric or injured spinal cord in mind. This study presents a...

Magnetic resonance imaging (MRI) is currently under investigation as a non-invasive tool to monitor neurodevelopmental trajectories and predict risk of cognitive deficits following white matter injury (WMI) in very preterm infants. In the present study, we evaluated the capacity of multimodal MRI (high-resolution T2-weighted imaging and diffusion t...

Most of our knowledge about the human spinal ascending (sensory) and descending (motor) pathways comes from non-invasive electrophysiological investigations. However, recent methodological advances in acquisition and analyses of functional magnetic resonance imaging (fMRI) data from the spinal cord, either alone or in combination with the brain, ha...

As the global health crisis unfolded, many academic conferences moved online in 2020. This move has been hailed as a positive step towards inclusivity in its attenuation of economic, physical, and legal barriers and effectively enabled many individuals from groups that have traditionally been underrepresented to join and participate. A number of st...

In a companion paper by Cohen-Adad et al . we introduce the spine generic quantitative MRI protocol that provides valuable metrics for assessing spinal cord macrostructural and microstructural integrity. This protocol was used to acquire a single subject dataset across 19 centers and a multi-subject dataset across 42 centers (for a total of 260 par...

Quantitative spinal cord (SC) magnetic resonance imaging (MRI) presents many challenges, including a lack of standardized imaging protocols. Here we present a prospectively harmonized quantitative MRI protocol, which we refer to as the spine generic protocol, for users of 3T MRI systems from the three main manufacturers: GE, Philips and Siemens. Th...

Background and purpose: Multi-parametric MRI, provides a variety of biomarkers sensitive to white matter integrity, However, spinal cord MRI data in pediatrics is rare compared to adults. The purpose of this work was 3-fold: 1) to develop a processing pipeline for atlas-based generation of the typically developing pediatric spinal cord WM tracts,...

We used 7 T MRI to: (i) characterize the grey and white matter pathology in the cervical spinal cord of patients with early relapsing-remitting and secondary progressive multiple sclerosis; (ii) assess the spinal cord lesion spatial distribution and the hypothesis of an outside-in pathological process possibly driven by CSF-mediated immune cytotoxi...

BACKGROUND AND PURPOSE Hereditary diffuse leukoencephalopathy with spheroids (HDLS) and multiple sclerosis (MS) are demyelinating and neurodegenerative disorders that can be hard to distinguish clinically and radiologically. HDLS is a rare disorder compared to MS, which has led to occurrent misdiagnosis of HDLS as MS. That is problematic since thei...

Spinal cord lesions detected on MRI hold important diagnostic and prognostic value for multiple sclerosis. Previous attempts to correlate lesion burden with clinical status have had limited success, however, suggesting that lesion location may be a contributor. Our aim was to explore the spatial distribution of multiple sclerosis lesions in the cer...

[This corrects the article DOI: 10.1371/journal.pone.0195733.].

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 atrophy and lesion burden, which are key criteria for the diagnosis, prognosis and longitudinal monitoring in MS. Achieving robust and reliable segmentation across multi...

Background Patients with mild degenerative cervical myelopathy (DCM) are often managed non-operatively, and surgery is recommended if neurological progression occurs. However, detection of progression is often subjective. Quantitative MRI (qMRI) directly measures spinal cord (SC) tissue changes, detecting axonal injury, demyelination, and atrophy....

Objectives Degenerative cervical myelopathy (DCM) involves extrinsic spinal cord compression causing tissue injury and neurological dysfunction. Asymptomatic spinal cord compression (ASCC) is more common, but its significance is poorly defined. This study investigates if: (1) ASCC can be automatically diagnosed using spinal cord shape analysis; (2)...

During the last two decades, MRI has been increasingly used for providing valuable quantitative information about spinal cord morphometry, such as quantification of the spinal cord atrophy in various diseases. However, despite the significant improvement of MR sequences adapted to the spinal cord, automatic image processing tools for spinal cord MR...

Template-based analysis of multi-parametric MRI data of the spinal cord sets the foundation for standardization and reproducibility, thereby helping the discovery of new biomarkers of spinal-related diseases. While MRI templates of the spinal cord have been recently introduced, none of them cover the entire spinal cord. In this study, we introduced...

Segmentation of grey matter in magnetic resonance images of the spinal cord is an important step in assessing disease state in neurological disorders such as multiple sclerosis. However, manual delineation of spinal cord tissue is time-consuming and susceptible to variability introduced by the rater. We present a novel segmentation method for spina...

Localizing the center of the spinal cord on MR images is a critical step toward fully automated and robust quantitative analysis, which is essential to achieve clinical utilization. While automatic localization of the spinal cord might appear as a simple task, that has already been addressed extensively, it is much more challenging to achieve this...

Background and purpose: T2*-weighted imaging provides sharp contrast between spinal cord GM and WM, allowing their segmentation and cross-sectional area measurement. Injured WM demonstrates T2*WI hyperintensity but requires normalization for quantitative use. We introduce T2*WI WM/GM signal-intensity ratio and compare it against cross-sectional ar...

Background and purpose: DTI, magnetization transfer, T2*-weighted imaging, and cross-sectional area can quantify aspects of spinal cord microstructure. However, clinical adoption remains elusive due to complex acquisitions, cumbersome analysis, limited reliability, and wide ranges of normal values. We propose a simple multiparametric protocol with...

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...

Brainhack events offer a novel workshop format with participant-generated content that caters to the rapidly growing open neuroscience community. Including components from hackathons and unconferences, as well as parallel educational sessions, Brainhack fosters novel collaborations around the interests of its attendees. Here we provide an overview...

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 de...

Introduction: Diffusion tensor imaging (DTI), magnetization transfer (MT), and T2*-weighted imaging measure aspects of spinal cord microstructure. This study investigates if these techniques can quantify injury to individual white matter (WM) tracts and correlate with focal neurological impairments in degenerative cervical myelopathy (DCM). Metho...

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...

Quantifying spinal cord (SC) atrophy in neurodegenerative and traumatic diseases brings important diagnosis and prognosis information for the clinician. We recently developed the PropSeg method, which allows for fast, accurate and automatic segmentation of the SC on different types of MRI contrast (e.g., T1-, T2- and T2*-weighted sequences) and any...

The field of spinal cord MRI is lacking a common template, as existing for the brain, which would allow extraction of multi-parametric data (diffusion-weighted, magnetization transfer, etc.) without user bias, thereby facilitating group analysis and multi-center studies. This paper describes a framework to produce an unbiased average anatomical tem...

Background / Purpose: Automatic spinal cord segmentation is crucial for large group multi-center study of spinal cord pathologies and lesions. Moreover, such a method should manage various multiple resolution (MR) contrast and different fields of view. Main conclusion: Accurate segmentation of the spinal cord was performed on T₁- an...

Spinal cord diseases or injuries can cause dysfunction of the sensory and locomotor systems. Segmentation of the spinal cord provides measures of atrophy and allows group analysis of multi-parametric MRI via inter-subject registration to a template. All these measures were shown to improve diagnostic and surgical intervention. We developed a framew...

This article introduces a novel structured light pattern designed to be compatible with the spatial light modulator (SLM) projection. The proposed pattern is a De Bruijn-based sequence applied to a combination of continuous and dashed lines for the pattern. The sequence is coded in the period and duty cycles of the dashed lines. It provides 16 diff...

This paper introduces a novel structured light pattern designed to be compatible with the hologram projection. The proposed pattern is a De Bruijn-based sequence applied to a combination of continuous and dashed lines for the pattern. The sequence is coded in the period in the period and duty cycles of the dashed lines. It provides 16 different lin...