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

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

Master's Research - Polytechnique Montréal
Co-supervisor :
PhD - Polytechnique Montréal
Co-supervisor :
PhD - Polytechnique Montréal
Master's Research - Polytechnique Montréal
PhD - Polytechnique Montréal
PhD - Polytechnique Montréal
Collaborating researcher
Research Intern - Polytechnique Montréal
Master's Research - Université de Montréal
Master's Research - Polytechnique Montréal
Postdoctorate - Polytechnique Montréal

Publications

Influence of scanning plane on Human Spinal Cord functional Magnetic Resonance echo planar imaging
Marta Moraschi
Silvia Tommasin
Laura Maugeri
Mauro DiNuzzo
Marco Masullo
Fabio Mangini
Lorenzo Giovannelli
Daniele Mascali
Tommaso Gili
Valerio Pisani
Ugo Nocentini
Federico Giove
Michela Fratini
BACKGROUND: Functional Magnetic Resonance Imaging (fMRI) is based on the Blood Oxygenation Level Dependent contrast and has been exploited f… (see more)or the indirect study of the neuronal activity within both the brain and the spinal cord. However, the interpretation of spinal cord fMRI (scfMRI) is still controversial and its diffusion is rather limited because of technical limitations. Overcoming these limitations would have a beneficial effect for the assessment and follow-up of spinal injuries and neurodegenerative diseases. PURPOSE: This study was aimed at systematically verify whether sagittal scanning in scfMRI using EPI readout is a viable alternative to the more common axial scanning, and at optimizing a pipeline for EPI-based scfMRI data analysis, based on Spinal Cord Toolbox (SCT). METHODS: Forty-five healthy subjects underwent MRI acquisition in a Philips Achieva 3T MRI scanner. T2*-weighted fMRI data were acquired using a GE-EPI sequence along sagittal and axial planes during an isometric motor task. Differences on benchmarks were assessed via paired two-sample t-test at p=0.05. RESULTS: We investigated the impact of the acquisition strategy by means of various metrics such as Temporal Signal to Noise Ratio (tSNR), Dice Coefficient to assess geometric distortions, Reproducibility and Sensitivity. tSNR was higher in axial than in sagittal scans, as well as reproducibility within the whole cord mask (t=7.4, p0.01) and within the GM mask (t=4.2, p0.01). The other benchmarks, associated with distortion and functional response, showed no differenc
Monitoring morphometric drift in lifelong learning segmentation of the spinal cord
Enamundram Naga Karthik
Sandrine B'edard
Jan Valovsek
Christoph Aigner
Elise Bannier
Josef Bednavr'ik
Virginie Callot
Anna Combes
Armin Curt
Gergely David
Falk Eippert
Lynn Farner
M. G. Fehlings
Patrick Freund
Tobias Granberg
Cristina Granziera
Rhscir Network Imaging Group
Ulrike Horn
Tom'avs Hor'ak
Suzanne Humphreys … (see 36 more)
Markus Hupp
Anne Kerbrat
Nawal Kinany
Shannon Kolind
Petr Kudlivcka
Anna Lebret
Lisa Eunyoung Lee
Caterina Mainero
Allan R. Martin
Megan McGrath
Govind Nair
Kristin P. O’Grady
Jiwon Oh
Russell Ouellette
Nikolai Pfender
Dario Pfyffer
P. Pradat
Alexandre Prat
Emanuele Pravatà
D. S. Reich
Ilaria Ricchi
Naama Rotem-Kohavi
Simon Schading-Sassenhausen
Maryam Seif
Andrew C. Smith
Seth Aaron Smith
Grace Sweeney
Roger Tam
Anthony Traboulsee
Constantina A. Treaba
Charidimos Tsagkas
Zachary Vavasour
Dimitri Van De Ville
Kenneth A. Weber
Impact of through‐slice gradient optimization for dynamic slice‐wise shimming in the cervico‐thoracic spinal cord
Arnaud Breheret
Alexandre D'Astous
Yixin Ma
Jason P. Stockmann
Rootlets-based registration to the spinal cord PAM50 template
Sandrine B'edard
Jan Valovsek
Valeria Oliva
Kenneth A. Weber
Spinal Cord Tract Integrity in Degenerative Cervical Myelopathy.
Newton Cho
Abdul Al-Shawwa
W. Bradley Jacobs
Nathan Evaniew
Jacques Bouchard
Steven Casha
Stephan duPlessis
Peter Lewkonia
Fred Nicholls
Alex Soroceanu
Ganesh Swamy
Kenneth C. Thomas
Michael M.H. Yang
David W. Cadotte
Addressing Missing Modality Challenges in MRI Images: A Comprehensive Review
Reza Azad
Mohammad Dehghanmanshadi
Nika Khosravi
Dorit Merhof
Normalizing Spinal Cord Compression Measures in Degenerative Cervical Myelopathy.
Sandrine Bédard
Jan Valošek
Maryam Seif
Armin Curt
Simon Schading-Sassenhausen
Nikolai Pfender
P. Freund
Markus Hupp
Considerations and recommendations from the ISMRM Diffusion Study Group for preclinical diffusion MRI: Part 3 -- Ex vivo imaging: data processing, comparisons with microscopy, and tractography
Kurt G Schilling
Amy F. D. Howard
Francesco Grussu
Andrada Ianus
Brian Hansen
Rachel L. C. Barrett
Manisha Aggarwal
Stijn Michielse
Fatima Nasrallah
Warda Syeda
Nian Wang
Jelle Veraart
Alard Roebroeck
Andrew F. Bagdasarian
Cornelius Eichner
Farshid Sepehrband
Jan Zimmermann
Lucas Soustelle
Christien Bowman
Benjamin C. Tendler … (see 38 more)
Andreea Hertanu
Ben Jeurissen
Marleen Verhoye
Lucio Frydman
Yohan van de Looij
David Hike
Jeff F. Dunn
Karla Miller
Bennett Landman
Noam Shemesh
Adam Anderson
Emilie McKinnon
Shawna Farquharson
Flavio Dell’ Acqua
Carlo Pierpaoli
Ivana Drobnjak
Alexander Leemans
Kevin D. Harkins
Maxime Descoteaux
Duan Xu
Hao Huang
Mathieu D. Santin
Samuel C. Grant
Andre Obenaus
Gene S. Kim
Dan Wu
Denis Le Bihan
Stephen J. Blackband
Luisa Ciobanu
Els Fieremans
Ruiliang Bai
Trygve B. Leergaard
Jiangyang Zhang
Tim B. Dyrby
G. Allan Johnson
Matthew D. Budde
Ileana O. Jelescu
Automatic segmentation of spinal cord lesions in MS: A robust tool for axial T2-weighted MRI scans
Enamundram Naga Karthik
J. McGinnis
R. Wurm
S. Ruehling
R. Graf
Jan Valošek
Pierre-Louis Benveniste
M. Lauerer
J. Talbott
R. Bakshi
S. Tauhid
T. Shepherd
A. Berthele
C. Zimmer
B. Hemmer
D. Rueckert
B. Wiestler
J. Kirschke
M. Muehlau
Deep learning models have achieved remarkable success in segmenting brain white matter lesions in multiple sclerosis (MS), becoming integral… (see more) to both research and clinical workflows. While brain lesions have gained significant attention in MS research, the involvement of spinal cord lesions in MS is relatively understudied. This is largely owed to the variability in spinal cord magnetic resonance imaging (MRI) acquisition protocols, high individual anatomical differences, the complex morphology and size of spinal cord lesions - and lastly, the scarcity of labeled datasets required to develop robust segmentation tools. As a result, automatic segmentation of spinal cord MS lesions remains a significant challenge. Although some segmentation tools exist for spinal cord lesions, most have been developed using sagittal T2-weighted (T2w) sequences primarily focusing on cervical spines. With the growing importance of spinal cord imaging in MS, axial T2w scans are becoming increasingly relevant due to their superior sensitivity in detecting lesions compared to sagittal acquisition protocols. However, most existing segmentation methods struggle to effectively generalize to axial sequences due to differences in image characteristics caused by the highly anisotropic spinal cord scans. To address these challenges, we developed a robust, open-source lesion segmentation tool tailored specifically for axial T2w scans covering the whole spinal cord. We investigated key factors influencing lesion segmentation, including the impact of stitching together individually acquired spinal regions, straightening the spinal cord, and comparing the effectiveness of 2D and 3D convolutional neural networks (CNNs). Drawing on these insights, we trained a multi-center model using an extensive dataset of 582 MS patients, resulting in a dataset comprising an entirety of 2,167 scans. We empirically evaluated the model's segmentation performance across various spinal segments for lesions with varying sizes. Our model significantly outperforms the current state-of-the-art methods, providing consistent segmentation across cervical, thoracic and lumbar regions. To support the broader research community, we integrate our model into the widely-used Spinal Cord Toolbox (v7.0 and above), making it accessible via the command sct_deepseg -task seg_sc_ms_lesion_axial_t2w -i .
Automatic segmentation of spinal cord lesions in MS: A robust tool for axial T2-weighted MRI scans
Enamundram Naga Karthik
Julian McGinnis
Ricarda Wurm
Sebastian Ruehling
Robert Graf
Jan Valošek
Pierre-Louis Benveniste
Markus Lauerer
Jason Talbott
Rohit Bakshi
Shahamat Tauhid
Timothy Shepherd
Achim Berthele
Claus Zimmer
Bernhard Hemmer
Daniel Rueckert
Benedikt Wiestler
Jan S. Kirschke
Mark Mühlau
Deep learning models have achieved remarkable success in segmenting brain white matter lesions in multiple sclerosis (MS), becoming integral… (see more) to both research and clinical workflows. While brain lesions have gained significant attention in MS research, the involvement of spinal cord lesions in MS is relatively understudied. This is largely owed to the variability in spinal cord magnetic resonance imaging (MRI) acquisition protocols, high individual anatomical differences, the complex morphology and size of spinal cord lesions - and lastly, the scarcity of labeled datasets required to develop robust segmentation tools. As a result, automatic segmentation of spinal cord MS lesions remains a significant challenge. Although some segmentation tools exist for spinal cord lesions, most have been developed using sagittal T2-weighted (T2w) sequences primarily focusing on cervical spines. With the growing importance of spinal cord imaging in MS, axial T2w scans are becoming increasingly relevant due to their superior sensitivity in detecting lesions compared to sagittal acquisition protocols. However, most existing segmentation methods struggle to effectively generalize to axial sequences due to differences in image characteristics caused by the highly anisotropic spinal cord scans. To address these challenges, we developed a robust, open-source lesion segmentation tool tailored specifically for axial T2w scans covering the whole spinal cord. We investigated key factors influencing lesion segmentation, including the impact of stitching together individually acquired spinal regions, straightening the spinal cord, and comparing the effectiveness of 2D and 3D convolutional neural networks (CNNs). Drawing on these insights, we trained a multi-center model using an extensive dataset of 582 MS patients, resulting in a dataset comprising an entirety of 2,167 scans. We empirically evaluated the model's segmentation performance across various spinal segments for lesions with varying sizes. Our model significantly outperforms the current state-of-the-art methods, providing consistent segmentation across cervical, thoracic and lumbar regions. To support the broader research community, we integrate our model into the widely-used Spinal Cord Toolbox (v7.0 and above), making it accessible via the command sct_deepseg -task seg_sc_ms_lesion_axial_t2w -i .
Multi-center benchmarking of cervical spinal cord RF coils for 7 T MRI: A traveling spines study
Eva Alonso‐Ortiz
Daniel Papp
Robert L. Barry
Kyota Poëti
Alan C. Seifert
Kyle M. Gilbert
Nibardo Lopez‐Rios
Jan Paska
Falk Eippert
Nikolaus Weiskopf
Laura Beghini
Nadine Graedel
Robert Trampel
Martina F Callaghan
Christoph S. Aigner
Patrick Freund
Maryam Seif
Aurélien Destruel
Virginie Callot
Johanna Vannesjo … (see 1 more)
Multi-center benchmarking of cervical spinal cord RF coils for 7 T MRI: A traveling spines study
Eva Alonso‐Ortiz
Daniel Papp
Robert L. Barry
Kyota Poëti
Alan C. Seifert
Kyle M. Gilbert
Nibardo Lopez‐Rios
Jan Paska
Falk Eippert
N. Weiskopf
Laura Beghini
Nadine Graedel
Robert Trampel
M. F. Callaghan
Christoph S Aigner
Patrick Freund
Maryam Seif
A. Destruel
Virginie Callot
Johanna Vannesjo … (see 1 more)
Purpose The depth within the body, small diameter, long length, and varying tissue surrounding the spinal cord impose specific consideration… (see more)s when designing radiofrequency coils. The optimal coil configuration for 7 T cervical spinal cord MRI is unknown and, currently, there are very few coil options. The purpose of this work was (1) to establish a quality control protocol for evaluating 7 T cervical spinal cord coils and (2) to use that protocol to evaluate the performance of 4 different coil designs. Methods Three healthy volunteers and a custom anthropomorphic phantom (the traveling spines cohort) were scanned at seven 7 T imaging centers using a common protocol and each center’s specific cervical spinal cord coil. Four different coil designs were tested (two in-house, one Rapid Biomedical, and one MRI.TOOLS design). Results The Rapid Biomedical coil was found to have the highest B1+ efficiency, whereas one of the in-house designs (NeuroPoly Lab) had the highest SNR and the largest spinal cord coverage. The MRI.TOOLS coil had the most uniform B1+ profile along the cervical spinal cord; however, it was limited in its ability to provide the requested flip angles (especially for larger individuals). The latter was also the case for the second in-house coil (MSSM). Conclusion The results of this study serve as a guide for the spinal cord MRI community in selecting the most suitable coil based on specific requirements and offer a standardized protocol for assessing future coils.