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
emvnagakarthik@gmail.com
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
abel.salmona@gmail.com
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

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
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
Calibration-free parallel transmission of the cervical, thoracic, and lumbar spinal cord at 7T.
Christoph S. Aigner
Manuel F. Sánchez Alarcon
Alexandre D'Astous
Eva Alonso‐Ortiz
Julien Cohen-Adad
Sebastian Schmitter
PURPOSE To address the limitations of spinal cord imaging at ultra-high field (UHF) due to time-consuming parallel transmit (pTx) adjustment… (see more)s. This study introduces calibration-free offline computed universal shim modes that can be applied seamlessly for different pTx RF coils and spinal cord target regions, substantially enhancing spinal cord imaging efficiency at UHF. METHODS A library of channel-wise relative B 1 +
2024-05-10
Magnetic Resonance in Medicine (published)
doi.org
Calibration-free parallel transmission of the cervical, thoracic, and lumbar spinal cord at 7T.
Christoph S. Aigner
Manuel F. Sánchez Alarcon
Alexandre D'Astous
Eva Alonso‐Ortiz
Julien Cohen-Adad
Sebastian Schmitter
PURPOSE To address the limitations of spinal cord imaging at ultra-high field (UHF) due to time-consuming parallel transmit (pTx) adjustment… (see more)s. This study introduces calibration-free offline computed universal shim modes that can be applied seamlessly for different pTx RF coils and spinal cord target regions, substantially enhancing spinal cord imaging efficiency at UHF. METHODS A library of channel-wise relative B 1 +
2024-05-10
Magnetic Resonance in Medicine (published)
doi.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
2024-05-10
Magnetic Resonance in Medicine (published)
doi.org
Calibration-free parallel transmission of the cervical, thoracic, and lumbar spinal cord at 7T.
Christoph S. Aigner
Manuel F. Sánchez Alarcon
Alexandre D'Astous
Eva Alonso‐Ortiz
Julien Cohen-Adad
Sebastian Schmitter
PURPOSE To address the limitations of spinal cord imaging at ultra-high field (UHF) due to time-consuming parallel transmit (pTx) adjustment… (see more)s. This study introduces calibration-free offline computed universal shim modes that can be applied seamlessly for different pTx RF coils and spinal cord target regions, substantially enhancing spinal cord imaging efficiency at UHF. METHODS A library of channel-wise relative B 1 +
2024-05-10
Magnetic Resonance in Medicine (published)
doi.org
Repeat it without me: Crowdsourcing the T1 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 … (see 22 more)
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
PURPOSE T1 mapping is a widely used quantitative MRI technique, but its tissue-specific values remain inconsistent across protocols, sites, … (see more)and vendors. The ISMRM Reproducible Research and Quantitative MR study groups jointly launched a challenge to assess the reproducibility of a well-established inversion-recovery T1 mapping technique, using acquisition details from a seminal T1 mapping paper on a standardized phantom and in human brains. METHODS The challenge used the acquisition protocol from Barral et al. (2010). Researchers collected T1 mapping data on the ISMRM/NIST phantom and/or in human brains. Data submission, pipeline development, and analysis were conducted using open-source platforms. Intersubmission and intrasubmission comparisons were performed. RESULTS 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). 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. CONCLUSION 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.
2024-05-10
Magnetic Resonance in Medicine (published)
doi.org
Repeat it without me: Crowdsourcing the T1 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 … (see 22 more)
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
T1 mapping is a widely used quantitative MRI technique, but its tissue‐specific values remain inconsistent across protocols, sites, and ve… (see more)ndors. The ISMRM Reproducible Research and Quantitative MR study groups jointly launched a challenge to assess the reproducibility of a well‐established inversion‐recovery T1 mapping technique, using acquisition details from a seminal T1 mapping paper on a standardized phantom and in human brains.
2024-05-10
Magnetic Resonance in Medicine (published)
doi.org
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
Julien Cohen-Adad
Michael G. Fehlings
Armin Curt
Maryam Seif
2024-05-07
European Journal of Neurology (published)
doi.org
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
Julien Cohen-Adad
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… (see more)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.
2024-05-07
European Journal of Neurology (published)
doi.org
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
Julien Cohen-Adad
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… (see more)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.
2024-05-07
European Journal of Neurology (published)
doi.org
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
Julien Cohen-Adad
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… (see more)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.
2024-05-07
European Journal of Neurology (published)
doi.org