Julien Cohen-Adad

Pierre Louis Benveniste

Doctorat - Polytechnique

Co-superviseur⋅e :

Doctorat - Polytechnique

Thomas Dagonneau

Maîtrise recherche - Polytechnique

Naga Karthik Enamundram

Doctorat - Polytechnique

Co-superviseur⋅e :

Maîtrise recherche - Polytechnique

Youssef Laatar

Maîtrise recherche - Polytechnique

Julien Laborde-Peyré

Stagiaire de recherche - Polytechnique

Nilser Laines Medina

Doctorat - Polytechnique

Nathan Molinier

Doctorat - Polytechnique

Kalum Ost

Collaborateur·rice de recherche

Arthur Toulouse

Maîtrise recherche - Polytechnique

Publications

Spinal cord demyelination predicts neurological deterioration in patients with mild degenerative cervical myelopathy

Abdul Al-Shawwa

Michael Craig

Kalum Ost

David Anderson

Steve Casha

W Bradley Jacobs

Nathan Evaniew

Saswati Tripathy

Jacques Bouchard

Peter Lewkonia

Fred Nicholls

Alex Soroceanu

Ganesh Swamy

Kenneth C Thomas

Stephan duPlessis

Michael MH Yang

Nicholas Dea

Jefferson R Wilson

David W Cadotte

Degenerative cervical myelopathy (DCM) is the most common form of atraumatic spinal cord injury globally. Clinical guidelines regarding surg… (voir plus)ery for patients with mild DCM and minimal symptoms remain uncertain. This study aims to identify imaging and clinical predictors of neurological deterioration in mild DCM and explore pathophysiological correlates to guide clinical decision-making. Patients with mild DCM underwent advanced MRI scans that included T2-weighted, diffusion tensor imaging and magnetisation transfer (MT) sequences, along with clinical outcome measures at baseline and 6-month intervals after enrolment. Quantitative MRI (qMRI) metrics were derived above and below maximally compressed cervical levels (MCCLs). Various machine learning (ML) models were trained to predict 6 month neurological deterioration, followed by global and local model interpretation to assess feature importance. A total of 49 patients were followed for a maximum of 2 years, contributing 110 6-month data entries. Neurological deterioration occurred in 38% of cases. The best-performing ML model, combining clinical and qMRI metrics, achieved a balanced accuracy of 83%, and an area under curve-receiver operating characteristic of 0.87. Key predictors included MT ratio (demyelination) above the MCCL in the dorsal and ventral funiculi and moderate tingling in the arm, shoulder or hand. qMRI metrics significantly improved predictive performance compared to models using only clinical (bal. acc=68.1%) or imaging data (bal. acc=57.4%). Reduced myelin content in the dorsal and ventral funiculi above the site of compression, combined with sensory deficits in the hands and gait/balance disturbances, predicts 6-month neurological deterioration in mild DCM and may warrant early surgical intervention.

2024-12-31

BMJ Neurology Open (publié)

Towards contrast-agnostic soft segmentation of the spinal cord

Sandrine Bédard

Enamundram Naga Karthik

Charidimos Tsagkas

Emanuele Pravatà

Cristina Granziera

Andrew Smith

Kenneth Arnold Weber II

Spinal cord segmentation is clinically relevant and is notably used to compute spinal cord cross-sectional area (CSA) for the diagnosis and … (voir plus)monitoring of cord compression or neurodegenerative diseases such as multiple sclerosis. While several semi and automatic methods exist, one key limitation remains: the segmentation depends on the MRI contrast, resulting in different CSA across contrasts. This is partly due to the varying appearance of the boundary between the spinal cord and the cerebrospinal fluid that depends on the sequence and acquisition parameters. This contrast-sensitive CSA adds variability in multi-center studies where protocols can vary, reducing the sensitivity to detect subtle atrophies. Moreover, existing methods enhance the CSA variability by training one model per contrast, while also producing binary masks that do not account for partial volume effects. In this work, we present a deep learning-based method that produces soft segmentations of the spinal cord. Using the Spine Generic Public Database of healthy participants (

2024-12-31

Medical Image Anal. (publié)

arxiv.org

TransCeption: Enhancing medical image segmentation with an inception-like transformer design for efficient feature fusion

Reza Azad

Yiwei Jia

Ehsan Khodapanah Aghdam

Dorit Merhof

2024-12-31

Comput. Vis. Media (publié)

Longitudinal reproducibility of brain and spinal cord quantitative MRI biomarkers

Mathieu Boudreau

Agah Karakuzu

Arnaud Boré

Basile Pinsard

Kiril Zelenkovski

Eva Alonso-Ortiz

Julie Boyle

Lune Bellec

Quantitative MRI (qMRI) promises better specificity, accuracy, repeatability, and reproducibility relative to its clinically-used qualitativ… (voir plus)e MRI counterpart. Longitudinal reproducibility is particularly important in qMRI. The goal is to reliably quantify tissue properties that may be assessed in longitudinal clinical studies throughout disease progression or during treatment. In this work, we present the initial data release of the quantitative MRI portion of the Courtois project on neural modelling (CNeuroMod), where the brain and cervical spinal cord of six participants were scanned at regular intervals over the course of several years. This first release includes 3 years of data collection and up to 10 sessions per participant using quantitative MRI imaging protocols (T1, magnetization transfer (MTR, MTsat), and diffusion). In the brain, T1MP2RAGE, fractional anisotropy (FA), mean diffusivity (MD), and radial diffusivity (RD) all exhibited high longitudinal reproducibility (intraclass correlation coefficient – ICC ≃ 1 and within-subject coefficient of variations – wCV 1%). The spinal cord cross-sectional area (CSA) computed using T2w images and T1MTsatexhibited the best longitudinal reproducibility (ICC ≃ 1 and 0.7 respectively, and wCV 2.4% and 6.9%). Results from this work show the level of longitudinal reproducibility that can be expected from qMRI protocols in the brain and spinal cord in the absence of hardware and software upgrades, and could help in the design of future longitudinal clinical studies.

2024-12-09

Imaging Neuroscience (publié)

SCIseg: Automatic Segmentation of Intramedullary Lesions in Spinal Cord Injury on T2-weighted MRI Scans

Enamundram Naga Karthik

Jan Valosek

Andrew C. Smith

Dario Pfyffer

Simon Schading-Sassenhausen

Lynn Farner

Kenneth A. Weber

Patrick Freund

The proposed deep learning model accurately segmented the spinal cord and spinal cord injury lesions in a diverse, multicenter dataset of T2… (voir plus)-weighted MRI scans.

2024-11-05

Radiology: Artificial Intelligence (publié)

Spinal cord evaluation in multiple sclerosis: clinical and radiological associations, present and future

B Mark Keegan

Martina Absinta

Eoin P Flanagan

Roland G Henry

Eric C Klawiter

Shannon Kolind

Stephen Krieger

Cornelia Laule

John A Lincoln

Steven Messina

Jiwon Oh

Nico Papinutto

Seth Aaron Smith

Anthony Traboulsee

2024-11-05

Brain Communications (publié)

Spiral volumetric optoacoustic tomography of reduced oxygen saturation in the spinal cord of M83 mouse model of Parkinson’s disease

Benjamin F. Combes

Sandeep Kumar Kalva

Pierre-Louis Benveniste

Agathe Tournant

Man Hoi Law

Joshua Newton

Maik Krüger

Rebecca Z. Weber

Inês Dias

Daniela Noain

Xose Luis Dean-Ben

Uwe Konietzko

Christian R. Baumann

Per-Göran Gillberg

Christoph Hock

Roger M. Nitsch

Daniel Razansky

Ruiqing Ni

Metabolism and bioenergetics in the central nervous system play important roles in the pathophysiology of Parkinson’s disease (PD). Here, … (voir plus)we employed a multimodal imaging approach to assess oxygenation changes in the spinal cord of the transgenic M83 murine model of PD overexpressing the mutated A53T alpha-synuclein form in comparison with non-transgenic littermates. In vivo spiral volumetric optoacoustic tomography (SVOT) was performed to assess oxygen saturation (sO2) in the spinal cords of M83 mice and non-transgenic littermates. Ex vivo high-field T1-weighted (T1w) magnetic resonance imaging (MRI) at 9.4T was used to assess volumetric alterations in the spinal cord. 3D SVOT analysis and deep learning-based automatic segmentation of T1w MRI data for the mouse spinal cord were developed for quantification. Immunostaining for phosphorylated alpha-synuclein (pS129 α-syn), as well as vascular organization (CD31 and GLUT1), was performed after MRI scan. In vivo SVOT imaging revealed a lower sO2SVOT in the spinal cord of M83 mice compared to non-transgenic littermates at sub-100 μm spatial resolution. Ex vivo MRI-assisted by in-house developed deep learning-based automatic segmentation (validated by manual analysis) revealed no volumetric atrophy in the spinal cord of M83 mice compared to non-transgenic littermates at 50 μm spatial resolution. The vascular network was not impaired in the spinal cord of M83 mice in the presence of pS129 α-syn accumulation. We developed tools for deep-learning-based analysis for the segmentation of mouse spinal cord structural MRI data, and volumetric analysis of sO2SVOT data. We demonstrated non-invasive high-resolution imaging of reduced sO2SVOT in the absence of volumetric structural changes in the spinal cord of PD M83 mouse model. The online version contains supplementary material available at 10.1007/s00259-024-06938-w.

2024-10-08

European Journal of Nuclear Medicine and Molecular Imaging (publié)

<scp>RF</scp> shimming in the cervical spinal cord at <scp>7 T</scp>

Daniel Papp

Kyle M. Gilbert

Gaspard Cereza

Alexandre D'Astous

Nibardo Lopez‐Rios

Mathieu Boudreau

Marcus J. Couch

Pedram Yazdanbakhsh

Robert L. Barry

Eva Alonso‐Ortiz

Julien Cohen‐Adad

The study's findings highlight the potential of RF shimming to advance 7 T MRI's clinical utility for central nervous system imaging by enab… (voir plus)ling more homogenous and efficient spinal cord imaging. Additionally, the research incorporates a reproducible Jupyter Notebook, enhancing the study's transparency and facilitating peer verification.

2024-08-12

Magnetic Resonance in Medicine (publié)

Myelin basic protein mRNA levels affect myelin sheath dimensions, architecture, plasticity, and density of resident glial cells

Hooman Bagheri

Hana Friedman

Amanda Hadwen

Celia Jarweh

Ellis Cooper

Lawrence Oprea

Claire Guerrier

Anmar Khadra

Armand Collin

Julien Cohen‐Adad

Amanda Young

Gerardo Mendez Victoriano

Matthew Swire

Andrew Jarjour

Marie E. Bechler

Rachel S. Pryce

Pierre Chaurand

Lise Cougnaud

Dajana Vuckovic

Elliott Wilion … (voir 11 de plus)

Owen Greene

Akiko Nishiyama

Anouk Benmamar‐Badel

Trevor Owens

Vladimir Grouza

Marius Tuznik

Hanwen Liu

David A. Rudko

Jinyi Zhang

Katherine A. Siminovitch

Alan C. Peterson

Myelin Basic Protein (MBP) is essential for both elaboration and maintenance of CNS myelin, and its reduced accumulation results in hypomyel… (voir plus)ination. How different Mbp mRNA levels affect myelin dimensions across the lifespan and how resident glial cells may respond to such changes are unknown. Here, to investigate these questions, we used enhancer‐edited mouse lines that accumulate Mbp mRNA levels ranging from 8% to 160% of wild type. In young mice, reduced Mbp mRNA levels resulted in corresponding decreases in Mbp protein accumulation and myelin sheath thickness, confirming the previously demonstrated rate‐limiting role of Mbp transcription in the control of initial myelin synthesis. However, despite maintaining lower line specific Mbp mRNA levels into old age, both MBP protein levels and myelin thickness improved or fully normalized at rates defined by the relative Mbp mRNA level. Sheath length, in contrast, was affected only when mRNA levels were very low, demonstrating that sheath thickness and length are not equally coupled to Mbp mRNA level. Striking abnormalities in sheath structure also emerged with reduced mRNA levels. Unexpectedly, an increase in the density of all glial cell types arose in response to reduced Mbp mRNA levels. This investigation extends understanding of the role MBP plays in myelin sheath elaboration, architecture, and plasticity across the mouse lifespan and illuminates a novel axis of glial cell crosstalk.

2024-07-17

Glia (publié)

Open Source in Lab Management

This document explores the advantages of integrating open source software and practices in managing a scientific lab, emphasizing reproducib… (voir plus)ility and the avoidance of pitfalls. It details practical applications from website management using GitHub Pages to organizing datasets in compliance with BIDS standards, highlights the importance of continuous testing for data integrity, IT management through Ansible for efficient system configuration, open source software development. The broader goal is to promote transparent, reproducible science by adopting open source tools. This approach not only saves time but exposes students to best practices, enhancing the transparency and reproducibility of scientific research.

2024-05-12

ArXiv (prépublication)

arxiv.org

Calibration‐free parallel transmission of the cervical, thoracic, and lumbar spinal cord at <scp>7T</scp>

Christoph S. Aigner

Manuel F. Sánchez Alarcon

Alexandre D'Astous

Eva Alonso‐Ortiz

Julien Cohen‐Adad

Sebastian Schmitter

The development of universal shims represents a significant advance by eliminating time‐consuming subject‐specific pTx adjustments. This… (voir plus) approach is expected to make UHF spinal cord imaging more accessible and user‐friendly, particularly for non‐pTx experts.

2024-05-09

Magnetic Resonance in Medicine (publié)

Repeat it without me: Crowdsourcing the T<sub>1</sub> mapping common ground via the ISMRM reproducibility challenge

Mathieu Boudreau

Agah Karakuzu

Julien Cohen‐Adad

Ecem Bozkurt

Madeline Carr

Marco Castellaro

Luis Concha

Mariya Doneva

Seraina A. Dual

Alex Ensworth

Alexandru Foias

Véronique Fortier

Refaat E. Gabr

Guillaume Gilbert

Carri K. Glide‐Hurst

Matthew Grech‐Sollars

Siyuan Hu

Oscar Jalnefjord

Jorge Jovicich

Kübra Keskin … (voir 22 de plus)

Peter Koken

Anastasia Kolokotronis

Simran Kukran

Nam G. Lee

Ives R. Levesque

Bochao Li

Dan Ma

Burkhard Mädler

Nyasha G. Maforo

Jamie Near

Erick Pasaye

Alonso Ramirez‐Manzanares

Ben Statton

Christian Stehning

Stefano Tambalo

Ye Tian

Chenyang Wang

Kilian Weiss

Niloufar Zakariaei

Shuo Zhang

Ziwei Zhao

Nikola Stikov

Eighteen submissions (39 phantom and 56 human datasets) on scanners by three MRI vendors were collected at 3 T (except one, at 0.35 T). … (voir plus)The mean coefficient of variation was 6.1% for intersubmission phantom measurements, and 2.9% for intrasubmission measurements. For humans, the intersubmission/intrasubmission coefficient of variation was 5.9/3.2% in the genu and 16/6.9% in the cortex. An interactive dashboard for data visualization was also developed: https://rrsg2020.dashboards.neurolibre.org.The T1 intersubmission variability was twice as high as the intrasubmission variability in both phantoms and human brains, indicating that the acquisition details in the original paper were insufficient to reproduce a quantitative MRI protocol. This study reports the inherent uncertainty in T1 measures across independent research groups, bringing us one step closer to a practical clinical baseline of T1 variations in vivo.

2024-05-09

Magnetic Resonance in Medicine (publié)