Julien Cohen-Adad

Paul Hoareau

Maîtrise recherche - Polytechnique

paul.hoareau@mila.quebec

youssef.laatar@mila.quebec

Youssef Laatar

Maîtrise recherche - Polytechnique

nathan.molinier@mila.quebec

Nathan Molinier

Doctorat - Polytechnique

Publications

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)

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

Patrick Freund

Viveka Boller

Tim M. Emmenegger

Muhammad Akbar

Markus Hupp

Nikolai Pfender

Claudia A. M. Gandini Wheeler-Kingshott

Michael G. Fehlings

Armin Curt

Maryam Seif

2024-05-06

European Journal of Neurology (publié)

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

Patrick Freund

Viveka Boller

Tim M. Emmenegger

Muhammad Akbar

Markus Hupp

Nikolai Pfender

Claudia A. M. Gandini Wheeler-Kingshott

Michael G. Fehlings

Armin Curt

Maryam Seif

Simultaneous assessment of neurodegeneration in both the cervical cord and brain across multiple centres can enhance the effectiveness of cl… (voir plus)inical 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.

2024-05-06

European Journal of Neurology (publié)

Body size interacts with the structure of the central nervous system: A multi-center in vivo neuroimaging study

René Labounek

Monica T. Bondy

Amy Paulson

Sandrine Bédard

Mihael Abramovic

Eva Alonso‐Ortiz

Nicole Atcheson

Laura Barlow

Robert Barry

Markus Barth

Marco Battiston

Christian Büchel

Matthew D. Budde

Virginie Callot

Anna Combes

Benjamin De Leener

Maxime Descoteaux

Paulo Loureiro de Sousa

Marek Dostál

Julien Doyon … (voir 73 de plus)

Adam Dvorak

Falk Eippert

Karla R. Epperson

Kevin Epperson

Patrick Freund

Jürgen Finsterbusch

Alexandru Foias

Michela Fratini

Issei Fukunaga

Claudia A. M. Gandini Wheeler‐Kingshott

Giancarlo Germani

Guillaume Gilbert

Federico Giove

Francesco Grussu

Akifumi Hagiwara

Pierre‐Gilles Henry

Tomáš Horák

Masaaki Hori

James M. Joers

Kouhei Kamiya

Haleh Karbasforoushan

Miloš Keřkovský

Ali Khatibi

Joo-Won Kim

Nawal Kinany

Hagen H. Kitzler

Shannon Kolind

Yazhuo Kong

Petr Kudlička

Paul Kuntke

Nyoman D. Kurniawan

Sławomir Kuśmia

Maria Marcella Laganà

Cornelia Laule

Christine Law

Tobias Leutritz

Yaou Liu

Sara Llufriú

Sean Mackey

Allan R. Martin

Eloy Martínez‐Heras

Loan Mattera

Kristin P. O’Grady

Nico Papinutto

Daniel S. Papp

Deborah Pareto

Todd B. Parrish

Anna Pichiecchio

Ferrán Prados

Àlex Rovira

Marc J. Ruitenberg

Rebecca S. Samson

Giovanni Savini

Maryam Seif

Alan C. Seifert

Alex K. Smith

Seth A. Smith

Zachary A. Smith

Elisabeth Solana

Yuichi Suzuki

George Tackley

Alexandra Tinnermann

Jan Valosek

Dimitri Van De Ville

Marios Yiannakas

Kenneth A. Weber

Nikolaus Weiskopf

Richard G. Wise

Patrik O. Wyss

Junqian Xu

Julien Cohen‐Adad

Christophe Lenglet

Igor Nestrašil

Clinical research emphasizes the implementation of rigorous and reproducible study designs that rely on between-group matching or controllin… (voir plus)g 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 importance of body size parameters in their relationship with spinal cord (SC) and brain magnetic resonance imaging (MRI) metrics. Data were derived from a cosmopolitan population of 267 healthy human adults (age 30.1±6.6 years old, 125 females). We show that body height correlated strongly or moderately with brain gray matter (GM) volume, cortical GM volume, total cerebellar volume, brainstem volume, and cross-sectional area (CSA) of cervical SC white matter (CSA-WM; 0.44≤r≤0.62). In comparison, age correlated weakly with cortical GM volume, precentral GM volume, and cortical thickness (−0.21≥r≥−0.27). Body weight correlated weakly with magnetization transfer ratio in the SC WM, dorsal columns, and lateral corticospinal tracts (−0.20≥r≥−0.23). Body weight further correlated weakly with the mean diffusivity derived from diffusion tensor imaging (DTI) in SC WM (r=−0.20) and dorsal columns (−0.21), but only in males. CSA-WM correlated strongly or moderately with brain volumes (0.39≤r≤0.64), and weakly with precentral gyrus thickness and DTI-based fractional anisotropy in SC dorsal columns and SC lateral corticospinal tracts (−0.22≥r≥−0.25). Linear mixture of sex and age explained 26±10% of data variance in brain volumetry and SC CSA. The amount of explained variance increased at 33±11% when body height was added into the mixture model. Age itself explained only 2±2% of such variance. In conclusion, body size is a significant biological variable. Along with sex and age, body size should therefore be included as a mandatory variable in the design of clinical neuroimaging studies examining SC and brain structure.

2024-04-30

bioRxiv (prépublication)

Influence of preprocessing, distortion correction and cardiac triggering on the quality of diffusion MR images of spinal cord

Kurt G. Schilling

Anna Combes

Karthik Ramadass

François Rheault

Grace Sweeney

Logan Prock

Subramaniam Sriram

Julien Cohen‐Adad

John C. Gore

Bennett A. Landman

Seth A. Smith

Kristin P. O’Grady

Diffusion MRI of the spinal cord (SC) is susceptible to geometric distortion caused by field inhomogeneities, and prone to misalignment acro… (voir plus)ss time series and signal dropout caused by biological motion. Several modifications of image acquisition and image processing techniques have been introduced to overcome these artifacts, but their specific benefits are largely unproven and warrant further investigations. We aim to evaluate two specific aspects of image acquisition and processing that address image quality in diffusion studies of the spinal cord: susceptibility corrections to reduce geometric distortions, and cardiac triggering to minimize motion artifacts. First, we evaluate 4 distortion preprocessing strategies on 7 datasets of the cervical and lumbar SC and find that while distortion correction techniques increase geometric similarity to structural images, they are largely driven by the high-contrast cerebrospinal fluid, and do not consistently improve the geometry within the cord nor improve white-to-gray matter contrast. We recommend at a minimum to perform bulk-motion correction in preprocessing and posit that improvements/adaptations are needed for spinal cord distortion preprocessing algorithms, which are currently optimized and designed for brain imaging. Second, we design experiments to evaluate the impact of removing cardiac triggering. We show that when triggering is foregone, images are qualitatively similar to triggered sequences, do not have increased prevalence of artifacts, and result in similar diffusion tensor indices with similar reproducibility to triggered acquisitions. When triggering is removed, much shorter acquisitions are possible, which are also qualitatively and quantitatively similar to triggered sequences. We suggest that removing cardiac triggering for cervical SC diffusion can be a reasonable option to save time with minimal sacrifice to image quality.

2024-04-30

Magnetic Resonance Imaging (publié)

Spinal cord perfusion impairments in the 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 a transgenic M83 murine model of PD in comparison to non-transgenic littermates at 9-12 months-of-age. A lower oxygen saturation (SO 2 ) SVOT was detected in vivo with spiral volumetric optoacoustic tomography (SVOT) in the spinal cord of M83 mice compared to non-transgenic littermate mice. Ex-vivo high-field T1-weighted magnetic resonance imaging (MRI) and immunostaining for alpha-synuclein (phospho-S129) and vascular organisation (CD31 and GLUT1) were used to investigate the nature of the abnormalities detected via in vivo imaging. Ex-vivo analysis showed that the vascular network in the spinal cord was not impaired in the spinal cord of M83 mice. Ex-vivo MRI assisted with deep learning-based automatic segmentation showed no volumetric atrophy in the spinal cord of M83 mice compared to non-transgenic littermates, whereas nuclear alpha-synuclein phosphorylated at Ser129 site could be linked to early pathology and metabolic dysfunction. The proposed and validated non-invasive high-resolution imaging tool to study oxygen saturation in the spinal cord of PD mice holds promise for assessing early changes preceding motor deficits in PD mice.

2024-04-28

bioRxiv (prépublication)

Contrast-agnostic Spinal Cord Segmentation: A Comparative Study of ConvNets and Vision Transformers

Enamundram Naga Karthik

Sandrine Bédard

Jan Valosek

A. Chandar