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
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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
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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
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Publications

Rapid simultaneous acquisition of macromolecular tissue volume, susceptibility, and relaxometry maps
Fang Frank Yu
Susie Yi Huang
Thomas Witzel
Ashwin Kumar
Congyu Liao
Tanguy Duval
Julien Cohen-Adad
Berkin Bilgic
Purpose A major obstacle to the clinical implementation of quantitative MR is the lengthy acquisition time required to derive multi-contrast… (see more) parametric maps. We sought to reduce the acquisition time for quantitative susceptibility mapping (QSM) and macromolecular tissue volume (MTV) by acquiring both contrasts simultaneously by leveraging their redundancies. The Joint Virtual Coil concept with generalized autocalibrating partially parallel acquisitions (JVC-GRAPPA) was applied to reduce acquisition time further. Methods Three adult volunteers were imaged on a 3T scanner using a multi-echo 3D GRE sequence acquired at three head orientations. MTV, QSM, R2*, T1, and proton density maps were reconstructed. The same sequence (GRAPPA R=4) was performed in subject #1 with a single head orientation for comparison. Fully sampled data was acquired in subject #2, from which retrospective undersampling was performed (R=6 GRAPPA and R=9 JVC-GRAPPA). Prospective undersampling was performed in subject #3 (R=6 GRAPPA and R=9 JVC-GRAPPA) using gradient blips to shift k-space sampling in later echoes. Results Subject #1’s multi-orientation and single-orientation MTV maps were not significantly different based on RMSE. For subject #2, the retrospectively undersampled JVC-GRAPPA and GRAPPA generated similar results as fully sampled data. This approach was validated with the prospectively undersampled images in subject #3. Using QSM, R2*, and MTV, the contributions of myelin and iron content to susceptibility was estimated. Conclusion We have developed a novel strategy to simultaneously acquire data for the reconstruction of five intrinsically co-registered 1-mm isotropic resolution multi-parametric maps, with a scan time of 6 minutes using JVC-GRAPPA.
2021-09-04
Magnetic Resonance in Medicine (published)
doi.org
Quantitative 7-Tesla Imaging of Cortical Myelin Changes in Early Multiple Sclerosis
Valeria Barletta
Elena Herranz
Constantina A. Treaba
Ambica Mehndiratta
Russell Ouellette
Gabriel Mangeat
Tobias Granberg
Jacob A. Sloane
Eric C Klawiter
Julien Cohen-Adad
Caterina Mainero
Cortical demyelination occurs early in multiple sclerosis (MS) and relates to disease outcome. The brain cortex has endogenous propensity fo… (see more)r remyelination as proven from histopathology study. In this study, we aimed at characterizing cortical microstructural abnormalities related to myelin content by applying a novel quantitative MRI technique in early MS. A combined myelin estimation (CME) cortical map was obtained from quantitative 7-Tesla (7T) T2* and T1 acquisitions in 25 patients with early MS and 19 healthy volunteers. Cortical lesions in MS patients were classified based on their myelin content by comparison with CME values in healthy controls as demyelinated, partially demyelinated, or non-demyelinated. At follow-up, we registered changes in cortical lesions as increased, decreased, or stable CME. Vertex-wise analysis compared cortical CME in the normal-appearing cortex in 25 MS patients vs. 19 healthy controls at baseline and investigated longitudinal changes at 1 year in 10 MS patients. Measurements from the neurite orientation dispersion and density imaging (NODDI) diffusion model were obtained to account for cortical neurite/dendrite loss at baseline and follow-up. Finally, CME maps were correlated with clinical metrics. CME was overall low in cortical lesions (p = 0.03) and several normal-appearing cortical areas (p 0.05) in the absence of NODDI abnormalities. Individual cortical lesion analysis revealed, however, heterogeneous CME patterns from extensive to partial or absent demyelination. At follow-up, CME overall decreased in cortical lesions and non-lesioned cortex, with few areas showing an increase (p 0.05). Cortical CME maps correlated with processing speed in several areas across the cortex. In conclusion, CME allows detection of cortical microstructural changes related to coexisting demyelination and remyelination since the early phases of MS, and shows to be more sensitive than NODDI and relates to cognitive performance.
2021-09-03
Frontiers in Neurology (published)
doi.org
Generic acquisition protocol for quantitative MRI of the spinal cord
Julien Cohen-Adad
Eva Alonso‐Ortiz
Mihael Abramovic
Carina Arneitz
Nicole Atcheson
Laura Barlow
Robert L. Barry
Markus Barth
Marco Battiston
Christian Büchel
Matthew D. Budde
Virginie Callot
Anna J. E. Combes
Benjamin De Leener
Maxime Descoteaux
Paulo Loureiro de Sousa
Marek Dostál
Julien Doyon
Adam Dvorak
Falk Eippert … (see 71 more)
Karla R. Epperson
Kevin S. Epperson
Patrick Freund
Jürgen Finsterbusch
Alexandru Foias
Michela Fratini
Issei Fukunaga
Claudia A. M. Gandini Wheeler-Kingshott
Giancarlo Germani
Guillaume Gilbert
Federico Giove
Charley Gros
Francesco Grussu
Akifumi Hagiwara
Pierre-Gilles Henry
Tomáš Horák
Masaaki Hori
James 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
Slawomir Kusmia
René Labounek
Maria Marcella Lagana
Cornelia Laule
Christine S. Law
Christophe Lenglet
Tobias Leutritz
Yaou Liu
Sara Llufriu
Sean Mackey
Eloy Martinez-Heras
Loan Mattera
Igor Nestrašil
Kristin P. O’Grady
Nico Papinutto
Daniel Papp
Deborah Pareto
Todd B. Parrish
Anna Pichiecchio
Ferran 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 Valošek
Dimitri Van De Ville
Marios C. Yiannakas
K. Weber
Nikolaus Weiskopf
Richard G. Wise
Patrik O. Wyss
Junqian Xu
2021-08-16
Nature Protocols (published)
doi.org
Open-access quantitative MRI data of the spinal cord and reproducibility across participants, sites and manufacturers
Julien Cohen-Adad
Eva Alonso‐Ortiz
Mihael Abramovic
Carina Arneitz
Nicole Atcheson
Laura Barlow
Robert L. Barry
Markus Barth
Marco Battiston
Christian Büchel
Matthew D. Budde
Virginie Callot
Anna J. E. Combes
Benjamin De Leener
Maxime Descoteaux
Paulo Loureiro de Sousa
Marek Dostál
Julien Doyon
Adam Dvorak
Falk Eippert … (see 71 more)
Karla R. Epperson
Kevin S. Epperson
Patrick Freund
Jürgen Finsterbusch
Alexandru Foias
Michela Fratini
Issei Fukunaga
Claudia A. M. Gandini Wheeler-Kingshott
Giancarlo Germani
Guillaume Gilbert
Federico Giove
Charley Gros
Francesco Grussu
Akifumi Hagiwara
Pierre-Gilles Henry
Tomáš Horák
Masaaki Hori
James 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
Slawomir Kusmia
René Labounek
Maria Marcella Lagana
Cornelia Laule
Christine S. Law
Christophe Lenglet
Tobias Leutritz
Yaou Liu
Sara Llufriu
Sean Mackey
Eloy Martinez-Heras
Loan Mattera
Igor Nestrašil
Kristin P. O’Grady
Nico Papinutto
Daniel Papp
Deborah Pareto
Todd B. Parrish
Anna Pichiecchio
Ferran 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
Y. Suzuki
George Tackley
Alexandra Tinnermann
Jan Valošek
Dimitri Van De Ville
Marios C. Yiannakas
Kenneth A. Weber
Nikolaus Weiskopf
Richard G. Wise
Patrik O. Wyss
Junqian Xu
2021-08-16
Scientific Data (published)
doi.org
Effectiveness of regional diffusion MRI measures in distinguishing multiple sclerosis abnormalities within the cervical spinal cord
Haykel Snoussi
Julien Cohen-Adad
Olivier Commowick
Benoit Combes
Elise Bannier
Slimane Tounekti
Anne Sophie Kerbrat
Christian Barillot
Emmanuel Caruyer
Multiple sclerosis (MS) is an inflammatory disorder of the central nervous system. Although conventional magnetic resonance imaging (MRI) is… (see more) widely used for MS diagnosis and clinical follow‐up, quantitative MRI has the potential to provide valuable intrinsic values of tissue properties that can enhance accuracy. In this study, we investigate the efficacy of diffusion MRI in distinguishing MS lesions within the cervical spinal cord, using a combination of metrics extracted from diffusion tensor imaging and Ball‐and‐Stick models.
2021-08-09
ArXiv (preprint)
doi.org
arxiv.org
Evaluation of distortion correction methods in diffusion MRI of the spinal cord
Haykel Snoussi
Emmanuel Caruyer
Julien Cohen-Adad
Olivier Commowick
Benoit Combes
Elise Bannier
Anne Kerbrat
Christian Barillot
2021-08-09
ArXiv (preprint)
arxiv.org
arxiv.org
Atlas-Based Quantification of DTI Measures in a Typically Developing Pediatric Spinal Cord
Shiva Shahrampour
Benjamin De Leener
Mahdi Alizadeh
D. Middleton
Laura Krisa
Adam E. Flanders
S. Faro
Julien Cohen-Adad
F. Mohamed
2021-07-29
American Journal of Neuroradiology (published)
doi.org
Automatic multiclass intramedullary spinal cord tumor segmentation on MRI with deep learning
Andreanne Lemay
Charley Gros
Zhizheng Zhuo
Jie Zhang
Yunyun Duan
Julien Cohen-Adad
Yaou Liu
2021-07-22
NeuroImage : Clinical (published)
doi.org
Diffusion magnetic resonance imaging reveals tract‐specific microstructural correlates of electrophysiological impairments in non‐myelopathic and myelopathic spinal cord compression
Jan Valošek
René Labounek
Tomáš Horák
Magda Horáková
Petr Bednařík
Miloš Keřkovský
Jan Kočica
Tomáš Rohan
Christophe Lenglet
Julien Cohen-Adad
Petr Hluštík
Eva Vlčková
Zdeněk Kadaňka
Josef Bednařík
Alena Svatkova
Non‐myelopathic degenerative cervical spinal cord compression (NMDC) frequently occurs throughout aging and may progress to potentially ir… (see more)reversible degenerative cervical myelopathy (DCM). Whereas standard clinical magnetic resonance imaging (MRI) and electrophysiological measures assess compression severity and neurological dysfunction, respectively, underlying microstructural deficits still have to be established in NMDC and DCM patients. The study aims to establish tract‐specific diffusion MRI markers of electrophysiological deficits to predict the progression of asymptomatic NMDC to symptomatic DCM.
2021-07-21
European Journal of Neurology (published)
doi.org
Dynamic shimming in the cervical spinal cord for multi-echo gradient-echo imaging at 3 T
Eva Alonso‐Ortiz
Daniel Papp
Alain D’astous
Julien Cohen-Adad
2021-07-21
ArXiv (preprint)
doi.org
arxiv.org
Rapid simultaneous acquisition of macromolecular tissue volume, susceptibility, and relaxometry maps
Fang Frank Yu
Susie Y. Huang
T. Witzel
Ashwin S. Kumar
Congyu Liao
Tanguy Duval
Julien Cohen-Adad
Berkin Bilgic
Purpose A major obstacle to the clinical implementation of quantitative MR is the lengthy acquisition time required to derive multi-contrast… (see more) parametric maps. We sought to reduce the acquisition time for quantitative susceptibility mapping (QSM) and macromolecular tissue volume (MTV) by acquiring both contrasts simultaneously by leveraging their redundancies. The Joint Virtual Coil concept with generalized autocalibrating partially parallel acquisitions (JVC-GRAPPA) was applied to reduce acquisition time further. Methods Three adult volunteers were imaged on a 3T scanner using a multi-echo 3D GRE sequence acquired at three head orientations. MTV, QSM, R2*, T1, and proton density maps were reconstructed. The same sequence (GRAPPA R=4) was performed in subject #1 with a single head orientation for comparison. Fully sampled data was acquired in subject #2, from which retrospective undersampling was performed (R=6 GRAPPA and R=9 JVC-GRAPPA). Prospective undersampling was performed in subject #3 (R=6 GRAPPA and R=9 JVC-GRAPPA) using gradient blips to shift k-space sampling in later echoes. Results Subject #1’s multi-orientation and single-orientation MTV maps were not significantly different based on RMSE. For subject #2, the retrospectively undersampled JVC-GRAPPA and GRAPPA generated similar results as fully sampled data. This approach was validated with the prospectively undersampled images in subject #3. Using QSM, R2*, and MTV, the contributions of myelin and iron content to susceptibility was estimated. Conclusion We have developed a novel strategy to simultaneously acquire data for the reconstruction of five intrinsically co-registered 1-mm isotropic resolution multi-parametric maps, with a scan time of 6 minutes using JVC-GRAPPA.
2021-06-09
bioRxiv (preprint)
doi.org
Quantitative magnetic resonance imaging of spinal cord microstructure in adults with cerebral palsy
Julien Cohen-Adad
The search for appropriate treatments of cerebral palsy (CP) would be facilitated if researchers could non-invasively monitor anatomical cha… (see more)nges in the spinal cord. The study by Trevarrow et al. aims to validate the relevance of magnetization transfer ratio and diffusion tensor imaging, both magnetic resonance imaging (MRI) techniques, to quantify microstructural abnormalities in the spinal cord of adult patients with CP. The authors used a semi-automated atlas-based analysis pipeline based on Spinal Cord Toolbox software to compute cord and gray matter atrophy and to quantify MRI metrics in specific spinal tracts. In line with their hypothesis, Trevarrow et al. observed differences in cord and gray matter size between participants with CP and typically developing peers. Interestingly, they also demonstrated an association between these morphometric biomarkers and clinical scores of hand dexterity. Magnetization transfer ratio was also reduced in the corticospinal tract of patients with CP. The study by Trevarrow et al. is a remarkable tour de force in that it is extremely difficult to image patients with CP as they are prone to motion (spasticity). In particular, gradient-echo sequences, used for magnetization transfer imaging, are particularly sensitive to motion, as can be seen on Figure 1b of the article. Echo planar imaging sequences, used for diffusion imaging, are sensitive to magnetic field inhomogeneities, which are prevalent in the spine region. The authors used an MRI acquisition protocol similar to a recently proposed standardized quantitative spinal cord MRI protocol (https://spine-generic.rtfd.io/), which likely helped them to obtain satisfactory images despite the many aforementioned challenges. From an image analysis standpoint, one limitation associated with atlas-based analysis (acknowledged by the authors) is that the registration to the template only relies on the spinal cord contour, not its internal structure. In other words, the white matter atlas is adjusted to the participant’s spinal cord contour, and the internal structure of the cord is quasi-linearly scaled (based on a B-spline regularized deformation). This quasi-linearity assumption might not hold true if, for example, the gray/white matter ratio differs between the participant and the template, and/ or the spatial location of the white matter tracts differs between the participant and the atlas, and/or specific tracts (e.g. corticospinal) degenerate. All these effects would cause a mismatch between the warped atlas’ and the participant’s white matter tracts. Unfortunately, there is no solution to this problem (yet). There are ways, however, to mitigate it. For example, using imaging sequences that are sensitive to some internal structures of the spinal cord, such as gray matter, or even some white matter tracts. These internal structures could then be accounted for during registration. However, these advanced contrast techniques are themselves noisy and sensitive to participant motion. In conclusion, the study by Trevarrow et al. is a remarkable technical achievement and a concrete first step towards the inclusion of microstructure MRI to the assessment of spinal cord integrity in patients with CP. Limitations, mostly related to data acquisition, could be tackled with the development of better solutions for gradient echo sequences in participants that are prone to motion. Navigator and/or advanced shimming approaches will hopefully mitigate these issues, making spinal cord quantitative MRI more amenable to clinical routine.
2021-05-15
Developmental Medicine & Child Neurology (published)
doi.org