Julien Cohen-Adad

thomas.dagonneau@mila.quebec

Thomas Dagonneau

Maîtrise recherche - Polytechnique

Naga Karthik Enamundram

Doctorat - Polytechnique

Co-superviseur⋅e :

Sarath Chandar

emvnagakarthik@gmail.com

Maîtrise recherche - Polytechnique

paul.hoareau@mila.quebec

youssef.laatar@mila.quebec

Youssef Laatar

Maîtrise recherche - Polytechnique

julien.laborde-peyre@mila.quebec

Julien Laborde-Peyré

Stagiaire de recherche - Polytechnique

nilser.lainesmedina@mila.quebec

Nilser Laines Medina

Doctorat - Polytechnique

Nathan Molinier

Doctorat - Polytechnique

nathan.molinier@mila.quebec

revillon.quentin@mila.quebec

Quentin Revillon

Stagiaire de recherche - Polytechnique

arthur.toulouse@mila.quebec

Arthur Toulouse

Maîtrise recherche - Polytechnique

Publications

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

Caterina Mainero

Cortical demyelination occurs early in multiple sclerosis (MS) and relates to disease outcome. The brain cortex has endogenous propensity fo… (voir plus)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.

2021-09-02

Frontiers in Neurology (publié)

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 Barry

Markus Barth

Marco Battiston

Christian Büchel

Matthew D. Budde

Virginie Callot

Anna Combes

Benjamin De Leener

Maxime Descoteaux

Paulo Loureiro de Sousa

Marek Dostál

Julien Doyon

Adam Dvorak

Falk Eippert … (voir 71 de plus)

Karla R. Epperson

Kevin 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 M. 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

Sławomir Kuśmia

René Labounek

Maria Marcella Laganà

Cornelia Laule

Christine Law

Christophe Lenglet

Tobias Leutritz

Yaou Liu

Sara Llufriú

Sean Mackey

Eloy Martínez‐Heras

Loan Mattera

Igor Nestrašil

Kristin P. O’Grady

Nico Papinutto

Daniel S. Papp

Deborah Pareto

Todd B. Parrish

Anna Pichiecchio

Ferrán 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 Valosek

Dimitri Van De Ville

Marios Yiannakas

Kenneth A. Weber

Nikolaus Weiskopf

Richard G. Wise

Patrik O. Wyss

Junqian Xu

Optimized and standardized MRI acquisition protocols for the spinal cord, compatible with Siemens, GE and Philips scanners.

2021-08-15

Nature Protocols (publié)

Open-access quantitative MRI data of the spinal cord and reproducibility across participants, sites and manufacturers

Eva Alonso-Ortiz

Mihael Abramovic

Carina Arneitz

Nicole Atcheson

Laura Barlow

Robert L. Barry

Markus Barth

Marco Battiston

Christian Büchel

Matthew Budde

Virginie Callot

Anna J. E. Combes

Benjamin De Leener

Maxime Descoteaux

Paulo Loureiro de Sousa

Marek Dostál

Julien Doyon

Adam Dvorak

Falk Eippert … (voir 71 de plus)

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 Laganà

Cornelia Laule

Christine S. Law

Christophe Lenglet

Tobias Leutritz

Yaou Liu

Sara Llufriú

Sean Mackey

Eloy Martinez-Heras

Loan Mattera

Igor Nestrašil

Kristin P. O'Grady

Nico Papinutto

Daniel Papp

Deborah Pareto

Todd B. Parrish

Anna Pichiecchio

Ferrán 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 Valosek

Dimitri Van De Ville

Marios C. Yiannakas

Kenneth A. Weber II

Nikolaus Weiskopf

Richard G. Wise

Patrik O. Wyss

Junqian Xu

In a companion paper by Cohen-Adad et al. we introduce the spine generic quantitative MRI protocol that provides valuable metrics for assess… (voir plus)ing spinal cord macrostructural and microstructural integrity. This protocol was used to acquire a single subject dataset across 19 centers and a multi-subject dataset across 42 centers (for a total of 260 participants), spanning the three main MRI manufacturers: GE, Philips and Siemens. Both datasets are publicly available via git-annex. Data were analysed using the Spinal Cord Toolbox to produce normative values as well as inter/intra-site and inter/intra-manufacturer statistics. Reproducibility for the spine generic protocol was high across sites and manufacturers, with an average inter-site coefficient of variation of less than 5% for all the metrics. Full documentation and results can be found at https://spine-generic.rtfd.io/. The datasets and analysis pipeline will help pave the way towards accessible and reproducible quantitative MRI in the spinal cord.

2021-08-15

Scientific Data (publié)

Evaluation of distortion correction methods in diffusion MRI of the spinal cord

Haykel Snoussi

Emmanuel Caruyer

Olivier Commowick

Benoit Combes

Élise Bannier

Anne Kerbrat

Christian Barillot

2021-08-08

ArXiv (prépublication)

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

F. Mohamed

2021-07-28

American Journal of Neuroradiology (publié)

Automatic multiclass intramedullary spinal cord tumor segmentation on MRI with deep learning

Andréanne Lemay

Charley Gros

Zhizheng Zhuo

Jie Zhang

Yunyun Duan

Yaou Liu

2021-07-21

NeuroImage : Clinical (publié)

Diffusion magnetic resonance imaging reveals tract‐specific microstructural correlates of electrophysiological impairments in non‐myelopathic and myelopathic spinal cord compression

Jan Valosek

René Labounek

Tomáš Horák

Magda Horáková

Petr Bednařík

Miloš Keřkovský

Jan Kočica

Tomáš Rohan

Christophe Lenglet

Julien Cohen‐Adad

Petr Hluštı́k

Eva Vlčková

Zdeněk Kadaňka

Josef Bednařík

Alena Svátková

Non‐myelopathic degenerative cervical spinal cord compression (NMDC) frequently occurs throughout aging and may progress to potentially ir… (voir plus)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.

2021-07-20

European Journal of Neurology (publié)

Quantitative magnetic resonance imaging of spinal cord microstructure in adults with cerebral palsy

The search for appropriate treatments of cerebral palsy (CP) would be facilitated if researchers could non-invasively monitor anatomical cha… (voir plus)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.

2021-05-14

Developmental Medicine & Child Neurology (publié)

Impact of individual rater style on deep learning uncertainty in medical imaging segmentation

Olivier Vincent

Charley Gros

While multiple studies have explored the relation between inter-rater variability and deep learning model uncertainty in medical segmentatio… (voir plus)n tasks, little is known about the impact of individual rater style. This study quantifies rater style in the form of bias and consistency and explores their impacts when used to train deep learning models. Two multi-rater public datasets were used, consisting of brain multiple sclerosis lesion and spinal cord grey matter segmentation. On both datasets, results show a correlation (

2021-05-04

ArXiv (prépublication)

arxiv.org

Associations Between Relative Morning Blood Pressure, Cerebral Blood Flow, and Memory in Older Adults Treated and Controlled for Hypertension

Adrián Noriega de la Colina

Atef Badji

Marie-Christine Robitaille-Grou

Christine Gagnon

Tommy Boshkovski

Maxime Lamarre-Cliche

Sven Joubert

Claudine J. Gauthier

Louis Bherer

Hélène Girouard

Supplemental Digital Content is available in the text. Hypertension, elevated morning blood pressure (BP) surges, and circadian BP variabili… (voir plus)ty constitute risk factors for cerebrovascular events. Nevertheless, while evidence indicates that hypertension is associated with cognitive dysfunctions, the link between BP variability and cognitive performance during aging is not clear. The purpose of this study is to determine the interaction between relative morning BP, cerebral blood flow (CBF) levels, and cognitive performance in hypertensive older adults with controlled BP under antihypertensive treatment. Eighty-four participants aged between 60 and 75 years old were separated into normotensive (n=51) and hypertensive (n=33) groups and underwent 24-hour ambulatory BP monitoring. They were also examined for CBF in the gray matter (CBF-GM) by magnetic resonance imaging and 5 cognitive domains: global cognition, working memory, episodic memory, processing speed, and executive functions. There was no difference in cognitive performance and CBF between normotensive and controlled hypertensive participants. Through a sensitivity analysis, we identified that, among relative morning BP variables, the best fit for CBF values in this cohort was the morning-evening difference in BP. The relative morning BP was negatively associated with CBF-GM in these hypertensive older adults only. In turn, CBF-GM levels were negatively associated with working and episodic memory scores in hypertensive older adults. This is the first extended study demonstrating an association between high relative morning BP and lower levels of CBF-GM, including the further impact of CBF-GM levels on the cognitive performance of specific domains in a community-based cohort of older adults with hypertension.

2021-04-30

Hypertension (publié)

Tracking white and grey matter degeneration along the spinal cord axis in degenerative cervical myelopathy

Kevin Vallotton

Gergely David

Markus Hupp

Nikolai Pfender

Michael Fehlings

Rebecca S. Samson

Claudia A. M. Gandini Wheeler-Kingshott

Armin Curt

Patrick Freund

Maryam Seif

Tissue-specific neurodegeneration revealed by quantitative MRI, already apparent across the spinal cord in mild-moderate DCM prior to the on… (voir plus)set of severe clinical impairments. WM microstructural changes are particularly sensitive to remote pathologically and clinically eloquent changes in DCM.

2021-04-21

medRxiv (prépublication)

ivadomed: A Medical Imaging Deep Learning Toolbox

Charley Gros

Andréanne Lemay

Olivier Vincent

Lucas Rouhier

Anthime Bucquet

ivadomed is an open-source Python package for designing, end-to-end training, and evaluating deep learning models applied to medical imaging… (voir plus) 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.

2021-02-11

Journal of Open Source Software (publié)