Portrait of Julien Cohen-Adad

Julien Cohen-Adad

Associate Academic Member
Associate Professor, Polytechnique Montréal, Electrical Engineering Department
Adjunct Professor, Université de Montréal, Department of Neuroscience
Research Topics
Medical Machine Learning
Website
Google Scholar
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Biography

Julien Cohen-Adad is a professor at Polytechnique Montréal and the associate director of the Neuroimaging Functional Unit at Université de Montréal. He is also the Canada Research Chair in Quantitative Magnetic Resonance Imaging.

His research focuses on advancing neuroimaging methods with the help of AI. Some examples of projects are:

- Multi-modal training for medical imaging tasks (segmentation of pathologies, diagnosis, etc.)

- Adding prior from MRI physics to improve model generalization

- Incorporating uncertainty measures to deal with inter-rater variability

- Continuous learning strategies when data sharing is restricted

- Bringing AI methods into clinical radiology routine via user-friendly software solutions

Cohen-Adad also leads multiple open-source software projects that are benefiting the research and clinical community (see neuro.polymtl.ca/software.html). In short, he loves MRI with strong magnets, neuroimaging, programming and open science!

Current Students

Rohan Banerjee
Master's Research - Polytechnique Montréal
Co-supervisor :
Gauthier Gidel
Website
Github
Google Scholar
Pierre Louis Benveniste
PhD - Polytechnique Montréal
Co-supervisor :
Hervé Lombaert
Website
Github
Google Scholar
Armand Collin
PhD - Polytechnique Montréal
Github
Thomas Dagonneau
Master's Research - Polytechnique Montréal
Github
Naga Karthik Enamundram
PhD - Polytechnique Montréal
Co-supervisor :
Sarath Chandar
[email protected]
Website
Github
Google Scholar
Nilser Laines Medina
PhD - Polytechnique Montréal
Nathan Molinier
PhD - Polytechnique Montréal
Github
Kalum Ost
Collaborating researcher
Abel Salmona Salmona
Research Intern - Polytechnique Montréal
[email protected]
Github
Julien Thouveny
Master's Research - Université de Montréal
Arthur Toulouse
Master's Research - Polytechnique Montréal
Github
Jan Valosek
Postdoctorate - Polytechnique Montréal
Website
Github
Google Scholar

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
Julien Cohen-Adad
Daniel Razansky
Ruiqing Ni
2024-10-09
European Journal of Nuclear Medicine and Molecular Imaging (published)
doi.org
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
Julien Cohen-Adad
Daniel Razansky
Ruiqing Ni
2024-10-09
European Journal of Nuclear Medicine and Molecular Imaging (published)
doi.org
RF shimming in the cervical spinal cord at 7 T.
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
PURPOSE Advancing the development of 7 T MRI for spinal cord imaging is crucial for the enhanced diagnosis and monitoring of various neurode… (see more)generative diseases and traumas. However, a significant challenge at this field strength is the transmit field inhomogeneity. Such inhomogeneity is particularly problematic for imaging the small, deep anatomical structures of the cervical spinal cord, as it can cause uneven signal intensity and elevate the local specific absorption ratio, compromising image quality. This multisite study explores several RF shimming techniques in the cervical spinal cord. METHODS Data were collected from 5 participants between two 7 T sites with a custom 8Tx/20Rx parallel transmission coil. We explored two radiofrequency (RF) shimming approaches from an MRI vendor and four from an open-source toolbox, showcasing their ability to enhance transmit field and signal homogeneity along the cervical spinal cord. RESULTS The circularly polarized (CP), coefficient of variation (CoV), and specific absorption rate (SAR) efficiency shim modes showed the highest B1 + efficiency, and the vendor-based "patient" and "volume" modes showed the lowest B1 + efficiency. The coefficient of variation method produced the highest CSF/spinal cord contrast on T2*-weighted scans (ratio of 1.27 ± 0.03), and the lowest variation of that contrast along the superior-inferior axis. CONCLUSION The study's findings highlight the potential of RF shimming to advance 7 T MRI's clinical utility for central nervous system imaging by enabling more homogenous and efficient spinal cord imaging. Additionally, the research incorporates a reproducible Jupyter Notebook, enhancing the study's transparency and facilitating peer verification.
2024-08-13
Magnetic Resonance in Medicine (published)
doi.org
<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
2024-08-13
Magnetic Resonance in Medicine (published)
doi.org
RF shimming in the cervical spinal cord at 7 T.
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
PURPOSE Advancing the development of 7 T MRI for spinal cord imaging is crucial for the enhanced diagnosis and monitoring of various neurode… (see more)generative diseases and traumas. However, a significant challenge at this field strength is the transmit field inhomogeneity. Such inhomogeneity is particularly problematic for imaging the small, deep anatomical structures of the cervical spinal cord, as it can cause uneven signal intensity and elevate the local specific absorption ratio, compromising image quality. This multisite study explores several RF shimming techniques in the cervical spinal cord. METHODS Data were collected from 5 participants between two 7 T sites with a custom 8Tx/20Rx parallel transmission coil. We explored two radiofrequency (RF) shimming approaches from an MRI vendor and four from an open-source toolbox, showcasing their ability to enhance transmit field and signal homogeneity along the cervical spinal cord. RESULTS The circularly polarized (CP), coefficient of variation (CoV), and specific absorption rate (SAR) efficiency shim modes showed the highest B1 + efficiency, and the vendor-based "patient" and "volume" modes showed the lowest B1 + efficiency. The coefficient of variation method produced the highest CSF/spinal cord contrast on T2*-weighted scans (ratio of 1.27 ± 0.03), and the lowest variation of that contrast along the superior-inferior axis. CONCLUSION The study's findings highlight the potential of RF shimming to advance 7 T MRI's clinical utility for central nervous system imaging by enabling more homogenous and efficient spinal cord imaging. Additionally, the research incorporates a reproducible Jupyter Notebook, enhancing the study's transparency and facilitating peer verification.
2024-08-13
Magnetic Resonance in Medicine (published)
doi.org
RF shimming in the cervical spinal cord at 7 T.
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
PURPOSE Advancing the development of 7 T MRI for spinal cord imaging is crucial for the enhanced diagnosis and monitoring of various neurode… (see more)generative diseases and traumas. However, a significant challenge at this field strength is the transmit field inhomogeneity. Such inhomogeneity is particularly problematic for imaging the small, deep anatomical structures of the cervical spinal cord, as it can cause uneven signal intensity and elevate the local specific absorption ratio, compromising image quality. This multisite study explores several RF shimming techniques in the cervical spinal cord. METHODS Data were collected from 5 participants between two 7 T sites with a custom 8Tx/20Rx parallel transmission coil. We explored two radiofrequency (RF) shimming approaches from an MRI vendor and four from an open-source toolbox, showcasing their ability to enhance transmit field and signal homogeneity along the cervical spinal cord. RESULTS The circularly polarized (CP), coefficient of variation (CoV), and specific absorption rate (SAR) efficiency shim modes showed the highest B1 + efficiency, and the vendor-based "patient" and "volume" modes showed the lowest B1 + efficiency. The coefficient of variation method produced the highest CSF/spinal cord contrast on T2*-weighted scans (ratio of 1.27 ± 0.03), and the lowest variation of that contrast along the superior-inferior axis. CONCLUSION The study's findings highlight the potential of RF shimming to advance 7 T MRI's clinical utility for central nervous system imaging by enabling more homogenous and efficient spinal cord imaging. Additionally, the research incorporates a reproducible Jupyter Notebook, enhancing the study's transparency and facilitating peer verification.
2024-08-13
Magnetic Resonance in Medicine (published)
doi.org
SCIsegV2: A Universal Tool for Segmentation of Intramedullary Lesions in Spinal Cord Injury
Enamundram Naga Karthik
Jan Valošek
Lynn Farner
Dario Pfyffer
Simon Schading-Sassenhausen
A. Lebret
Gergely David
Andrew Smith
Kenneth A. Weber
Maryam Seif
Rhscir Network Imaging Group
Patrick Freund
Julien Cohen-Adad
Spinal cord injury (SCI) is a devastating incidence leading to permanent paralysis and loss of sensory-motor functions potentially resulting… (see more) in the formation of lesions within the spinal cord. Imaging biomarkers obtained from magnetic resonance imaging (MRI) scans can predict the functional recovery of individuals with SCI and help choose the optimal treatment strategy. Currently, most studies employ manual quantification of these MRI-derived biomarkers, which is a subjective and tedious task. In this work, we propose (i) a universal tool for the automatic segmentation of intramedullary SCI lesions, dubbed \texttt{SCIsegV2}, and (ii) a method to automatically compute the width of the tissue bridges from the segmented lesion. Tissue bridges represent the spared spinal tissue adjacent to the lesion, which is associated with functional recovery in SCI patients. The tool was trained and validated on a heterogeneous dataset from 7 sites comprising patients from different SCI phases (acute, sub-acute, and chronic) and etiologies (traumatic SCI, ischemic SCI, and degenerative cervical myelopathy). Tissue bridges quantified automatically did not significantly differ from those computed manually, suggesting that the proposed automatic tool can be used to derive relevant MRI biomarkers. \texttt{SCIsegV2} and the automatic tissue bridges computation are open-source and available in Spinal Cord Toolbox (v6.4 and above) via the \texttt{sct\_deepseg -task seg\_sc\_lesion\_t2w\_sci} and \texttt{sct\_analyze\_lesion} functions, respectively.
2024-07-24
ArXiv (preprint)
doi.org
arxiv.org
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 … (see 11 more)
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
Abstract Myelin Basic Protein (MBP) is essential for both elaboration and maintenance of CNS myelin, and its reduced accumulation results in… (see more) hypomyelination. 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.
2024-07-18
Glia (published)
doi.org
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 … (see 11 more)
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
Abstract Myelin Basic Protein (MBP) is essential for both elaboration and maintenance of CNS myelin, and its reduced accumulation results in… (see more) hypomyelination. 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.
2024-07-18
Glia (published)
doi.org
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 … (see 11 more)
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
2024-07-18
Glia (published)
doi.org
Automatic Segmentation of the Spinal Cord Nerve Rootlets
Jan Valošek
Theo Mathieu
Raphaëlle Schlienger
Olivia S. Kowalczyk
Julien Cohen-Adad
Precise identification of spinal nerve rootlets is relevant to delineate spinal levels for the study of functional activity in the spinal co… (see more)rd. The goal of this study was to develop an automatic method for the semantic segmentation of spinal nerve rootlets from T2-weighted magnetic resonance imaging (MRI) scans. Images from two open-access MRI datasets were used to train a 3D multi-class convolutional neural network using an active learning approach to segment C2-C8 dorsal nerve rootlets. Each output class corresponds to a spinal level. The method was tested on 3T T2-weighted images from datasets unseen during training to assess inter-site, inter-session, and inter-resolution variability. The test Dice score was 0.67 +- 0.16 (mean +- standard deviation across rootlets levels), suggesting a good performance. The method also demonstrated low inter-vendor and inter-site variability (coefficient of variation= 1.41 %), as well as low inter-session variability (coefficient of variation= 1.30 %) indicating stable predictions across different MRI
2024-07-02
Imaging Neuroscience (published)
doi.org
arxiv.org
Open Source in Lab Management
Julien Cohen-Adad
This document explores the advantages of integrating open source software and practices in managing a scientific lab, emphasizing reproducib… (see more)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.
2024-05-13
ArXiv (preprint)
doi.org
arxiv.org