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

PhD - Polytechnique Montréal
Master's Research - Polytechnique Montréal
Master's Research - Polytechnique Montréal
Master's Research - Polytechnique Montréal
PhD - Polytechnique Montréal
Master's Research - Polytechnique Montréal

Publications

SCIseg: Automatic Segmentation of T2-weighted Hyperintense Lesions in Spinal Cord Injury
Andrew C. Smith
Dario Pfyffer
Simon Schading-Sassenhausen
Lynn Farner
Kenneth A. Weber II
Patrick Freund
Background: Quantitative MRI biomarkers in spinal cord injury (SCI) can help understand the extent of the focal injury. However, due to the … (see more)lack of automatic segmentation methods, these biomarkers are derived manually, which is a time-consuming process prone to intra- and inter-rater variability, thus limiting large multi-site studies and translation to clinical workflows. Purpose: To develop a deep learning tool for the automatic segmentation of T2-weighted hyperintense lesions and the spinal cord in SCI patients. Material and Methods: This retrospective study included a cohort of SCI patients from three sites enrolled between July 2002 and February 2023 who underwent clinical MRI examination. A deep learning model, SCIseg, was trained on T2-weighted images with heterogeneous image resolutions (isotropic, anisotropic), and orientations (axial, sagittal) acquired using scanners from different manufacturers (Siemens, Philips, GE) and different field strengths (1T, 1.5T, 3T) for the automatic segmentation of SCI lesions and the spinal cord. The proposed method was visually and quantitatively compared with other open-source baseline methods. Quantitative biomarkers (lesion volume, lesion length, and maximal axial damage ratio) computed from manual ground-truth lesion masks and automatic SCIseg predictions were correlated with clinical scores (pinprick, light touch, and lower extremity motor scores). A between-group comparison was performed using the Wilcoxon signed-rank test. Results: MRI data from 191 SCI patients (mean age, 48.1 years {+/-} 17.9 [SD]; 142 males) were used for training. Compared to existing methods, SCIseg achieved the best segmentation performance for both the cord and lesions and generalized well to both traumatic and non-traumatic SCI patients. SCIseg is open-source and accessible through the Spinal Cord Toolbox. Conclusion: Automatic segmentation of intramedullary lesions commonly seen in traumatic SCI replaces the tedious manual annotation process and enables the extraction of relevant lesion morphometrics in large cohorts. The proposed model generalizes across lesion etiologies (traumatic, ischemic), scanner manufacturers and heterogeneous image resolutions.
Reproducible Spinal Cord Quantitative MRI Analysis with the Spinal Cord Toolbox
The spinal cord plays a pivotal role in the central nervous system, providing communication between the brain and the body and containing cr… (see more)itical motor and sensory networks. Recent advancements in spinal cord MRI data acquisition and image analysis have shown a potential to improve the diagnostics, prognosis, and management of a variety of pathological conditions. In this review, we first discuss the significance of standardized spinal cord MRI acquisition protocol in multi-center and multi-manufacturer studies. Then, we cover open-access spinal cord MRI datasets, which are important for reproducible science and validation of new methods. Finally, we elaborate on the recent advances in spinal cord MRI data analysis techniques implemented in the open-source software package Spinal Cord Toolbox (SCT).
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
Élise Bannier
Slimane Tounekti
Anne 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.
Pontomedullary junction as a reference for spinal cord cross-sectional area: validation across neck positions
Maxime Bouthillier
Spinal cord cross-sectional area (CSA) is an important MRI biomarker to assess spinal cord atrophy in various neurodegenerative and traumati… (see more)c spinal cord diseases. However, the conventional method of computing CSA based on vertebral levels is inherently flawed, as the prediction of spinal levels from vertebral levels lacks reliability, leading to considerable variability in CSA measurements. Computing CSA from an intrinsic neuroanatomical reference, the pontomedullary junction (PMJ), has been proposed in previous work to overcome limitations associated with using a vertebral reference. However, the validation of this alternative approach, along with its variability across and within participants under variable neck extensions, remains unexplored. The goal of this study was to determine if the variability of CSA across neck flexions/extensions is reduced when using the PMJ, compared to vertebral levels. Ten participants underwent a 3T MRI T2w isotropic scan at 0.6 mm3 for 3 neck positions: extension, neutral and flexion. Spinal cord segmentation, vertebral labeling, PMJ labeling, and CSA were computed automatically while spinal segments were labeled manually. Mean coefficient of variation for CSA across neck positions was 3.99 ± 2.96% for the PMJ method vs. 4.02 ± 3.01% for manual spinal segment method vs. 4.46 ± 3.10% for the disc method. These differences were not statistically significant. The PMJ method was slightly more reliable than the disc-based method to compute CSA at specific spinal segments, although the difference was not statistically significant. This suggests that the PMJ can serve as a valuable alternative and reliable method for estimating CSA when a disc-based approach is challenging or not feasible, such as in cases involving fused discs in individuals with spinal cord injuries.
An 8-channel Tx dipole and 20-channel Rx loop coil array for MRI of the cervical spinal cord at 7 Tesla
Nibardo Lopez-Rios
Kyle M. Gilbert
Daniel Papp
Gaspard Cereza
Alexandru Foias
Deshpande Rangaprakash
Markus W. May
Bastien Guerin
Lawrence L. Wald
Boris Keil
Jason P. Stockmann
Robert L. Barry
The quality of cervical spinal cord images can be improved by the use of tailored radiofrequency coil solutions for ultra-high field imaging… (see more); however, very few commercial and research 7 Tesla radiofrequency coils currently exist for the spinal cord, and in particular those with parallel transmit capabilities. This work presents the design, testing and validation of a pTx/Rx coil for the human neck and cervical/upper-thoracic spinal cord. The pTx portion is composed of 8 dipoles to ensure high homogeneity over this large region of the spinal cord. The Rx portion is made of 20 semi-adaptable overlapping loops to produce high Signal-to-noise ratio (SNR) across the patient population. The coil housing is designed to facilitate patient positioning and comfort, while being tight fitting to ensure high sensitivity. We demonstrate RF shimming capabilities to optimize B1+ uniformity, power efficiency and/or specific absorption rate (SAR) efficiency. B1+ homogeneity, SNR and g-factor was evaluated in adult volunteers and demonstrated excellent performance from the occipital lobe down to the T4-T5 level. We compared the proposed coil with two state-of-the-art head and head/neck coils, confirming its superiority in the cervical and upper-thoracic regions of the spinal cord. This coil solution therefore provides a convincing platform for producing the high image quality necessary for clinical and research scanning of the upper spinal cord.
Enhancing Medical Image Segmentation with TransCeption: A Multi-Scale Feature Fusion Approach
Reza Azad
Yiwei Jia
Ehsan Khodapanah Aghdam
Dorit Merhof
While CNN-based methods have been the cornerstone of medical image segmentation due to their promising performance and robustness, they suff… (see more)er from limitations in capturing long-range dependencies. Transformer-based approaches are currently prevailing since they enlarge the reception field to model global contextual correlation. To further extract rich representations, some extensions of the U-Net employ multi-scale feature extraction and fusion modules and obtain improved performance. Inspired by this idea, we propose TransCeption for medical image segmentation, a pure transformer-based U-shape network featured by incorporating the inception-like module into the encoder and adopting a contextual bridge for better feature fusion. The design proposed in this work is based on three core principles: (1) The patch merging module in the encoder is redesigned with ResInception Patch Merging (RIPM). Multi-branch transformer (MB transformer) adopts the same number of branches as the outputs of RIPM. Combining the two modules enables the model to capture a multi-scale representation within a single stage. (2) We construct an Intra-stage Feature Fusion (IFF) module following the MB transformer to enhance the aggregation of feature maps from all the branches and particularly focus on the interaction between the different channels of all the scales. (3) In contrast to a bridge that only contains token-wise self-attention, we propose a Dual Transformer Bridge that also includes channel-wise self-attention to exploit correlations between scales at different stages from a dual perspective. Extensive experiments on multi-organ and skin lesion segmentation tasks present the superior performance of TransCeption compared to previous work. The code is publicly available at https://github.com/mindflow-institue/TransCeption.
Label fusion and training methods for reliable representation of inter-rater uncertainty
Charley Gros
Enamundram Naga Karthik
Medical tasks are prone to inter-rater variability due to multiple factors such as image quality, professional experience and training, or g… (see more)uideline clarity. Training deep learning networks with annotations from multiple raters is a common practice that mitigates the model's bias towards a single expert. Reliable models generating calibrated outputs and reflecting the inter-rater disagreement are key to the integration of artificial intelligence in clinical practice. Various methods exist to take into account different expert labels. We focus on comparing three label fusion methods: STAPLE, average of the rater's segmentation, and random sampling of each rater's segmentation during training. Each label fusion method is studied using both the conventional training framework and the recently published SoftSeg framework that limits information loss by treating the segmentation task as a regression. Our results, across 10 data splittings on two public datasets, indicate that SoftSeg models, regardless of the ground truth fusion method, had better calibration and preservation of the inter-rater rater variability compared with their conventional counterparts without impacting the segmentation performance. Conventional models, i.e., trained with a Dice loss, with binary inputs, and sigmoid/softmax final activate, were overconfident and underestimated the uncertainty associated with inter-rater variability. Conversely, fusing labels by averaging with the SoftSeg framework led to underconfident outputs and overestimation of the rater disagreement. In terms of segmentation performance, the best label fusion method was different for the two datasets studied, indicating this parameter might be task-dependent. However, SoftSeg had segmentation performance systematically superior or equal to the conventionally trained models and had the best calibration and preservation of the inter-rater variability.
HiFormer: Hierarchical Multi-scale Representations Using Transformers for Medical Image Segmentation
Moein Heidari
Amirhossein Kazerouni
Milad Soltany
Reza Azad
Ehsan Khodapanah Aghdam
Dorit Merhof
Convolutional neural networks (CNNs) have been the consensus for medical image segmentation tasks. However, they suffer from the limitation … (see more)in modeling long-range dependencies and spatial correlations due to the nature of convolution operation. Although transformers were first developed to address this issue, they fail to capture low-level features. In contrast, it is demonstrated that both local and global features are crucial for dense prediction, such as segmenting in challenging contexts. In this paper, we propose HiFormer, a novel method that efficiently bridges a CNN and a transformer for medical image segmentation. Specifically, we design two multi-scale feature representations using the seminal Swin Transformer module and a CNN-based encoder. To secure a fine fusion of global and local features obtained from the two aforementioned representations, we propose a Double-Level Fusion (DLF) module in the skip connection of the encoder-decoder structure. Extensive experiments on various medical image segmentation datasets demonstrate the effectiveness of HiFormer over other CNN-based, transformer-based, and hybrid methods in terms of computational complexity, and quantitative and qualitative results. Our code is publicly available at: https://github.com/amirhossein-kz/HiFormer
ivadomed: A Medical Imaging Deep Learning Toolbox
ivadomed is an open-source Python package for designing, end-to-end training, and evaluating deep learning models applied to medical imaging… (see more) data. The package includes APIs, command-line tools, documentation, and tutorials. ivadomed also includes pre-trained models such as spinal tumor segmentation and vertebral labeling. Original features of ivadomed include a data loader that can parse image metadata (e.g., acquisition parameters, image contrast, resolution) and subject metadata (e.g., pathology, age, sex) for custom data splitting or extra information during training and evaluation. Any dataset following the Brain Imaging Data Structure (BIDS) convention will be compatible with ivadomed without the need to manually organize the data, which is typically a tedious task. Beyond the traditional deep learning methods, ivadomed features cutting-edge architectures, such as FiLM and HeMis, as well as various uncertainty estimation methods (aleatoric and epistemic), and losses adapted to imbalanced classes and non-binary predictions. Each step is conveniently configurable via a single file. At the same time, the code is highly modular to allow addition/modification of an architecture or pre/post-processing steps. Example applications of ivadomed include MRI object detection, segmentation, and labeling of anatomical and pathological structures. Overall, ivadomed enables easy and quick exploration of the latest advances in deep learning for medical imaging applications. ivadomed's main project page is available at https://ivadomed.org.
Biomedical image analysis competitions: The state of current participation practice
Matthias Eisenmann
Annika Reinke
Vivienn Weru
Minu Dietlinde Tizabi
Fabian Isensee
T. Adler
PATRICK GODAU
Veronika Cheplygina
Michal Kozubek
Sharib Ali
Anubha Gupta
Jan. Kybic
Alison Professor Noble
Carlos Ortiz de Sol'orzano
Samiksha Pachade
Caroline Petitjean
Daniel Sage
Donglai Wei
Elizabeth Wilden
Deepak Alapatt … (see 334 more)
Vincent Andrearczyk
Ujjwal Baid
Spyridon Bakas
Niranjan Balu
Sophia Bano
Vivek Singh Bawa
Jorge Bernal
Sebastian Bodenstedt
Alessandro Casella
Jinwook Choi
Olivier Commowick
M. Daum
Adrien Depeursinge
Reuben Dorent
J. Egger
H. Eichhorn
Sandy Engelhardt
Melanie Ganz
Gabriel Girard
Lasse Donovan Hansen
Mattias Paul Heinrich
Nicholas Heller
Alessa Hering
Arnaud Huaulm'e
Hyunjeong Kim
Bennett Landman
Hongwei Bran Li
Jianning Li
Junfang Ma
Anne L. Martel
Carlos Mart'in-Isla
Bjoern Menze
Chinedu Innocent Nwoye
Valentin Oreiller
Nicolas Padoy
Sarthak Pati
Kelly Payette
Carole H. Sudre
K. V. Wijnen
Armine Vardazaryan
Tom Kamiel Magda Vercauteren
Martin Wagner
Chuanbo Wang
Moi Hoon Yap
Zeyun Yu
Chuner Yuan
Maximilian Zenk
Aneeq Zia
David Zimmerer
Rina Bao
Chanyeol Choi
Andrew Cohen
Oleh Dzyubachyk
Adrian Galdran
Tianyuan Gan
Tianqi Guo
Pradyumna Gupta
M. Haithami
Edward Ho
Ikbeom Jang
Zhili Li
Zheng Luo
Filip Lux
Sokratis Makrogiannis
Dominikus Muller
Young-Tack Oh
Subeen Pang
Constantin Pape
Gorkem Polat
Charlotte Rosalie Reed
Kanghyun Ryu
Tim Scherr
Vajira L. Thambawita
Haoyu Wang
Xinliang Wang
Kele Xu
H.-I. Yeh
Doyeob Yeo
Yi Yuan
Yan Zeng
Xingwen Zhao
Julian Ronald Abbing
Jannes Adam
Nagesh Adluru
Niklas Agethen
S. Ahmed
Yasmina Al Khalil
Mireia Alenya
Esa J. Alhoniemi
C. An
Talha E Anwar
Tewodros Arega
Netanell Avisdris
D. Aydogan
Yi-Shi Bai
Maria Baldeon Calisto
Berke Doga Basaran
Marcel Beetz
Cheng Bian
Hao-xuan Bian
Kevin Blansit
Louise Bloch
Robert Bohnsack
Sara Bosticardo
J. Breen
Mikael Brudfors
Raphael Brungel
Mariano Cabezas
Alberto Cacciola
Zhiwei Chen
Yucong Chen
Dan Chen
Minjeong Cho
Min-Kook Choi
Chuantao Xie Chuantao Xie
Dana Cobzas
Jorge Corral Acero
Sujit Kumar Das
Marcela de Oliveira
Hanqiu Deng
Guiming Dong
Lars Doorenbos
Cory Efird
Di Fan
Mehdi Fatan Serj
Alexandre Fenneteau
Lucas Fidon
Patryk Filipiak
Ren'e Finzel
Nuno Renato Freitas
C. Friedrich
Mitchell J. Fulton
Finn Gaida
Francesco Galati
Christoforos Galazis
Changna Gan
Zheyao Gao
Sheng Gao
Matej Gazda
Beerend G. A. Gerats
Neil Getty
Adam Gibicar
Ryan J. Gifford
Sajan Gohil
Maria Grammatikopoulou
Daniel Grzech
Orhun Guley
Timo Gunnemann
Chun-Hai Guo
Sylvain Guy
Heonjin Ha
Luyi Han
Ilseok Han
Ali Hatamizadeh
Tianhai He
Ji-Wu Heo
Sebastian Hitziger
SeulGi Hong
Seungbum Hong
Rian Huang
Zi-You Huang
Markus Huellebrand
Stephan Huschauer
M. Hussain
Tomoo Inubushi
Ece Isik Polat
Mojtaba Jafaritadi
Seonghun Jeong
Bailiang Jian
Yu Jiang
Zhifan Jiang
Yu Jin
Smriti Joshi
A. Kadkhodamohammadi
R. A. Kamraoui
Inhak Kang
Jun-Su Kang
Davood Karimi
April Ellahe Khademi
Muhammad Irfan Khan
Suleiman A. Khan
Rishab Khantwal
Kwang-Ju Kim
Timothy Lee Kline
Satoshi Kondo
Elina Kontio
Adrian Krenzer
Artem Kroviakov
Hugo J. Kuijf
Satyadwyoom Kumar
Francesco La Rosa
Abhishek Lad
Doohee Lee
Minho Lee
Chiara Lena
Hao Li
Ling Li
Xingyu Li
F. Liao
Kuan-Ya Liao
Arlindo L. Oliveira
Chaonan Lin
Shanhai Lin
Akis Linardos
M. Linguraru
Han Liu
Tao Liu
Dian Liu
Yanling Liu
Joao Lourencco-Silva
Jing Lu
Jia Lu
Imanol Luengo
Christina Bach Lund
Huan Minh Luu
Yingqi Lv
Leon Maechler
L. SinaMansour
Kenji Marshall
Moona Mazher
Richard McKinley
Alfonso Medela
Felix Meissen
Mingyuan Meng
Dylan Bradley Miller
S. Mirjahanmardi
Arnab Kumar Mishra
Samir Mitha
Hassan Mohy-ud-Din
Tony C. W. Mok
Gowtham Krishnan Murugesan
Enamundram Naga Karthik
Sahil Nalawade
Jakub Nalepa
M. Naser
Ramin Nateghi
Hammad Naveed
Quang-Minh Nguyen
Cuong Nguyen Quoc
Bruno Oliveira
David Owen
Jimut Bahan Pal
Junwen Pan
Wei-Dong Pan
Winnie Pang
Bogyu Park
Vivek G. Pawar
Kamlesh Pawar
Michael Peven
Lena Philipp
Tomasz Pieciak
Szymon S Płotka
Marcel Plutat
Fattane Pourakpour
Domen Prelovznik
K. Punithakumar
Abdul Qayyum
Sandro Queir'os
Arman Rahmim
Salar Razavi
Jintao Ren
Mina Rezaei
Jonathan Adam Rico
ZunHyan Rieu
Markus Rink
Johannes Roth
Yusely Ruiz-gonzalez
Numan Saeed
Anindo Saha
Mostafa M. Sami Salem
Ricardo Sanchez-matilla
Kurt G Schilling
Weizhen Shao
Zhiqiang Shen
Ruize Shi
Pengcheng Shi
Daniel Sobotka
Th'eodore Soulier
Bella Specktor Fadida
D. Stoyanov
Timothy Sum Hon Mun
Xiao-Fu Sun
Rong Tao
Franz Thaler
Antoine Th'eberge
Felix Thielke
Helena R. Torres
K. Wahid
Jiacheng Wang
Yifei Wang
Wei David Wang
Xiong Jun Wang
Jianhui Wen
Ning Wen
Marek Wodziński
Yehong Wu
Fangfang Xia
Tianqi Xiang
Cheng Xiaofei
Lizhang Xu
Tingting Xue
Yu‐Xia Yang
Lingxian Yang
Kai Yao
Huifeng Yao
Amirsaeed Yazdani
Michael Yip
Hwa-Seong Yoo
Fereshteh Yousefirizi
Shu-Fen Yu
Lei Yu
Jonathan Zamora
Ramy A. Zeineldin
Dewen Zeng
Jianpeng Zhang
Bokai Zhang
Jiapeng Zhang
Fangxi Zhang
Huahong Zhang
Zhongchen Zhao
Zixuan Zhao
Jia Zhao
Can Zhao
Qiuyue Zheng
Yuheng Zhi
Ziqi Zhou
Baosheng Zou
Klaus Maier-Hein
PAUL F. JÄGER
Annette Kopp-Schneider
Lena Maier-Hein
Histology-informed automatic parcellation of white matter tracts in the rat spinal cord
Harris Nami
Christian S. Perone
The white matter is organized into “tracts” or “bundles,” which connect different parts of the central nervous system. Knowing where… (see more) these tracts are located in each individual is important for understanding the cause of potential sensorial, motor or cognitive deficits and for developing appropriate treatments. Traditionally, tracts are found using tracer injection, which is a difficult, slow and poorly scalable technique. However, axon populations from a given tract exhibit specific characteristics in terms of morphometrics and myelination. Hence, the delineation of tracts could, in principle, be done based on their morphometry. The objective of this study was to generate automatic parcellation of the rat spinal white matter tracts using the manifold information from scanning electron microscopy images of the entire spinal cord. The axon morphometrics (axon density, axon diameter, myelin thickness and g-ratio) were computed pixelwise following automatic axon segmentation using AxonSeg. The parcellation was based on an agglomerative clustering algorithm to group the tracts. Results show that axon morphometrics provide sufficient information to automatically identify some white matter tracts in the spinal cord, however, not all tracts were correctly identified. Future developments of microstructure quantitative MRI even bring hope for a personalized clustering of white matter tracts in each individual patient. The generated atlas and the associated code can be found at https://github.com/neuropoly/tract-clustering.
Shimming toolbox: An open‐source software toolbox for <scp>B0</scp> and <scp>B1</scp> shimming in MRI
Alexandre D'Astous
Gaspard Cereza
Daniel Papp
Kyle M. Gilbert
Jason P. Stockmann
Eva Alonso‐Ortiz
Julien Cohen‐Adad
Introduce Shimming Toolbox ( https://shimming‐toolbox.org), an open‐source software package for prototyping new methods and performing s… (see more)tatic, dynamic, and real‐time B0 shimming as well as B1 shimming experiments. Shimming Toolbox features various field mapping techniques, manual and automatic masking for the brain and spinal cord, B0 and B1 shimming capabilities accessible through a user‐friendly graphical user interface. Validation of Shimming Toolbox was demonstrated in three scenarios: (i) B0 dynamic shimming in the brain at 7T using custom AC/DC coils, (ii) B0 real‐time shimming in the spinal cord at 3T, and (iii) B1 static shimming in the spinal cord at 7T. Shimming Toolbox provides an open‐source platform where researchers can collaborate, prototype and conveniently test B0 and B1 shimming experiments. Future versions will include additional field map preprocessing techniques, optimization algorithms, and compatibility across multiple MRI manufacturers.