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 electrophysiological assessments as predictive markers of lower limb motor recovery after spinal cord injury: a pilot study with an adaptive trial design

Yin Nan Huang

El-Mehdi Meftah

Charlotte H. Pion

Jean-Marc Mac-Thiong

Dorothy Barthélemy

Observational, cohort study. (1) Determine the feasibility and relevance of assessing corticospinal, sensory, and spinal pathways early aft… (voir plus)er traumatic spinal cord injury (SCI) in a rehabilitation setting. (2) Validate whether electrophysiological and magnetic resonance imaging (MRI) measures taken early after SCI could identify preserved neural pathways, which could then guide therapy. Intensive functional rehabilitation hospital (IFR). Five individuals with traumatic SCI and eight controls were recruited. The lower extremity motor score (LEMS), electrical perceptual threshold (EPT) at the S2 dermatome, soleus (SOL) H-reflex, and motor evoked potentials (MEPs) in the tibialis anterior (TA) muscle were assessed during the stay in IFR and in the chronic stage (>6 months post-SCI). Control participants were only assessed once. Feasibility criteria included the absence of adverse events, adequate experimental session duration, and complete dataset gathering. The relationship between electrophysiological data collected in IFR and LEMS in the chronic phase was studied. The admission MRI was used to calculate the maximal spinal cord compression (MSCC). No adverse events occurred, but a complete dataset could not be collected for all subjects due to set-up configuration limitations and time constraints. EPT measured at IFR correlated with LEMS in the chronic phases (r = −0.67), whereas SOL H/M ratio, H latency, MEPs and MSCC did not. Adjustments are necessary to implement electrophysiological assessments in an IFR setting. Combining MRI and electrophysiological measures may lead to better assessment of neuronal deficits early after SCI.

2022-02-23

Spinal Cord Series and Cases (publié)

Advanced Diffusion MR Imaging for Multiple Sclerosis in the Brain and Spinal Cord

Masaaki Hori

Tomoko Maekawa

Kouhei Kamiya

Akifumi Hagiwara

Masami Goto

Mariko Yoshida Takemura

Shohei Fujita

Christina Andica

Koji Kamagata

Shigeki Aoki

Diffusion tensor imaging (DTI) has been established its usefulness in evaluating normal-appearing white matter (NAWM) and other lesions that… (voir plus) are difficult to evaluate with routine clinical MRI in the evaluation of the brain and spinal cord lesions in multiple sclerosis (MS), a demyelinating disease. With the recent advances in the software and hardware of MRI systems, increasingly complex and sophisticated MRI and analysis methods, such as q-space imaging, diffusional kurtosis imaging, neurite orientation dispersion and density imaging, white matter tract integrity, and multiple diffusion encoding, referred to as advanced diffusion MRI, have been proposed. These are capable of capturing in vivo microstructural changes in the brain and spinal cord in normal and pathological states in greater detail than DTI. This paper reviews the current status of recent advanced diffusion MRI for assessing MS in vivo as part of an issue celebrating two decades of magnetic resonance in medical sciences (MRMS), an official journal of the Japanese Society of Magnetic Resonance in Medicine.

2022-02-14

Magnetic Resonance in Medical Sciences (publié)

Erratum to: Rapid simultaneous acquisition of macromolecular tissue volume, susceptibility, and relaxometry maps (Magn Reson Med. 2022;87:781‐790.)

Fang Frank Yu

Susie Yi Huang

Ashwin Kumar

Thomas Witzel

Congyu Liao

Tanguy Duval

Berkin Bilgic

2022-02-09

Magnetic Resonance in Medicine (publié)

Brain-spinal cord interaction in long-term motor sequence learning in human: An fMRI study

Ali Khatibi

Shahabeddin Vahdat

Ovidiu Lungu

Jürgen Finsterbusch

Christian Büchel

Veronique Marchand-Pauvert

Julien Doyon

2021-12-31

NeuroImage (publié)

Titre: Title: Comparison of Myelin Imaging Techniques in Ex Vivo Spinal Cord Auteur:

Nikola Stikov

Manh-Tung Vuong

Vuong Manh Tung

Myelin is a dielectric material that wraps around the axons of nerve fibers to enable fast conduction of signals throughout the nervous syst… (voir plus)em. Loss of myelin can cause anywhere from minor interruption to complete disruption of nerve impulses in a range of neurodegenerative diseases such as multiple sclerosis and Parkinson’s disease. There is an ongoing debate in the myelin imaging community about which biomarker based on Magnetic Resonance Imaging (MRI) is more correlated with myelin. In this work, we implemented and compared several MRI-based myelin imaging techniques (quantitative magnetization transfer imaging, myelin water imaging, and proton density imaging) by evaluating their repeatability and their relation to large-scale histology in the ex vivo spinal cords of a rat, a dog, and a human. While there are studies investigating the relationship between pairs of them as well as with histology, to the best of our knowledge, this is the first study that implemented and compared all those methods at the same time to evaluate their reproducibility and their correlation with myelin. Qualitatively the contrasts were similar, and all techniques had comparable scan-rescan and correlations with histology. Surprisingly, the voxel-wise correlations between the various myelin measures were almost as high as the scan-rescan correlations. The correlations decreased when only white matter was considered, which could be due to the small dynamic range of the measurement, or due to artifacts related to the preparation and panoramic scanning of the tissue. We conclude that the myelin imaging techniques explored in this thesis exhibit similar specificity to myelin, yet the histological correlations suggest that more work is needed to determine the optimal myelin imaging protocol. The study also pointed out some potential miscalibrations during acquisitions as well as data processing that may lead to anywhere from minor to major impact on the accuracy of the results. These include B1 mapping, insufficient spoiling and variation of the predelay time. We have also standardized the data processing routines by upgrading qMTLab to qMRLab which adds several quantitative MR methods to the toolbox, such as standard T1 mapping and field mapping. In addition, the data of the dog spinal cord in this study will be published together with the analysis scripts to help the interested reader to reproduce the findings from this thesis.

2021-12-31

(publié)

www.semanticscholar.org

The Myelin-Weighted Connectome in Parkinson's Disease

Tommy Boshkovski

Bratislav Misic

Isabelle Arnulf

Jean-Christophe Corvol

Marie Vidailhet

Stéphane Lehéricy

Nikola Stikov

Matteo Mancini

Even though Parkinson's disease (PD) is typically viewed as largely affecting gray matter, there is growing evidence that there are also str… (voir plus)uctural changes in the white matter. Traditional connectomics methods that study PD may not be specific to underlying microstructural changes, such as myelin loss. The primary objective of this study is to investigate the PD‐induced changes in myelin content in the connections emerging from the basal ganglia and the brainstem. For the weighting of the connectome, we used the longitudinal relaxation rate as a biologically grounded myelin‐sensitive metric. We computed the myelin‐weighted connectome in 35 healthy control subjects and 81 patients with PD. We used partial least squares to highlight the differences between patients with PD and healthy control subjects. Then, a ring analysis was performed on selected brainstem and subcortical regions to evaluate each node's potential role as an epicenter for disease propagation. Then, we used behavioral partial least squares to relate the myelin alterations with clinical scores. Most connections (~80%) emerging from the basal ganglia showed a reduced myelin content. The connections emerging from potential epicentral nodes (substantia nigra, nucleus basalis of Meynert, amygdala, hippocampus, and midbrain) showed significant decrease in the longitudinal relaxation rate (P 0.05). This effect was not seen for the medulla and the pons. The myelin‐weighted connectome was able to identify alteration of the m

2021-12-21

Movement Disorders (inconnu)

Reduced Axon Calibre in the Associative Striatum of the Sapap3 Knockout Mouse

Eliana Lopes Rio da Silva Lousada

Mathieu Boudreau

Julien Cohen‐Adad

Brahim Nait‐Oumesmar

Eric Burguière

Christiane Schreiweis

Pathological repetitive behaviors are a common feature of different neuropsychiatric disorders such as obsessive-compulsive disorder or Gill… (voir plus)es de la Tourette syndrome. The Sapap3 knockout mouse (Sapap3-KO) is the current reference model used in translational psychiatry to study co-morbid repetitive behaviors, presenting both compulsive-like as well as tic-like behaviors. Consistent with clinical and fundamental research literature relating compulsive-like symptoms to associative cortico-striatal dysfunctions and tic-like symptoms to sensorimotor cortico-striatal dysfunctions, abnormalities comprising both circuits have been described in this mouse model. Findings reported on these mice point towards not only macro-, but also micro-circuitry deficits, both of which can be affected by neuronal structural changes. As such, in the present study, we aimed to investigate structural changes in associative and sensorimotor striatal areas that could affect information conduction. We used AxonDeepSeg, an open-source software to automatically segment and measure myelin thickness and axon caliber, and found that axon caliber, the main contributor for changes in conduction speed, is specifically reduced in the associative but not the sensorimotor striatum of the Sapap3-KO mouse. This smaller axon caliber in Sapap3-KO mice is not a general neuronal feature of this region, but specific to a subpopulation of axons with large caliber. These results point to a primary structural deficit in the associative striatum, affecting signal conduction and consequent connectivity.

2021-10-13

Brain Sciences (publié)

Minimum detectable spinal cord atrophy with automatic segmentation: Investigations using an open-access dataset of healthy participants

Paul Bautin

•Evaluate the robustness of an automated analysis pipeline for detecting SC atrophy.•Simulate spinal cord atrophy and scan-rescan variab… (voir plus)ility.•Fully automated analysis method available on an open access database.•Evaluation of sample size and inter/intra-subject variability for T1w and T2w images. Evaluate the robustness of an automated analysis pipeline for detecting SC atrophy. Simulate spinal cord atrophy and scan-rescan variability. Fully automated analysis method available on an open access database. Evaluation of sample size and inter/intra-subject variability for T1w and T2w images.

2021-10-03

NeuroImage : Clinical (publié)

Author Correction: 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 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 … (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

Nikolaus Weiskopf

Richard G. Wise

Patrik O. Wyss

Junqian Xu

2021-09-22

Scientific Data (publié)

Stacked Hourglass Network with a Multi-level Attention Mechanism: Where to Look for Intervertebral Disc Labeling

Reza Azad

Lucas Rouhier

Labeling vertebral discs from MRI scans is important for the proper diagnosis of spinal related diseases, including multiple sclerosis, amyo… (voir plus)trophic lateral sclerosis, degenerative cervical myelopathy and cancer. Automatic labeling of the vertebral discs in MRI data is a difficult task because of the similarity between discs and bone area, the variability in the geometry of the spine and surrounding tissues across individuals, and the variability across scans (manufacturers, pulse sequence, image contrast, resolution and artefacts). In previous studies, vertebral disc labeling is often done after a disc detection step and mostly fails when the localization algorithm misses discs or has false positive detection. In this work, we aim to mitigate this problem by reformulating the semantic vertebral disc labeling using the pose estimation technique. To do so, we propose a stacked hourglass network with multi-level attention mechanism to jointly learn intervertebral disc position and their skeleton structure. The proposed deep learning model takes into account the strength of semantic segmentation and pose estimation technique to handle the missing area and false positive detection. To further improve the performance of the proposed method, we propose a skeleton-based search space to reduce false positive detection. The proposed method evaluated on spine generic public multi-center dataset and demonstrated better performance comparing to previous work, on both T1w and T2w contrasts. The method is implemented in ivadomed (https://ivadomed.org).

2021-09-20

Machine Learning in Medical Imaging (publié)

arxiv.org

Team NeuroPoly: Description of the Pipelines for the MICCAI 2021 MS New Lesions Segmentation Challenge

Uzay Macar

Enamundram Naga Karthik

Charley Gros

Andréanne Lemay

This paper gives a detailed description of the pipelines used for the 2nd edition of the MICCAI 2021 Challenge on Multiple Sclerosis Lesion … (voir plus)Segmentation. An overview of the data preprocessing steps applied is provided along with a brief description of the pipelines used, in terms of the architecture and the hyperparameters. Our code for this work can be found at: https://github.com/ivadomed/ms-challenge-2021.

2021-09-11

ArXiv (prépublication)

arxiv.org

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

Berkin Bilgic

Purpose A major obstacle to the clinical implementation of quantitative MR is the lengthy acquisition time required to derive multi-contrast… (voir plus) 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.

2021-09-03

Magnetic Resonance in Medicine (publié)