Julien Cohen-Adad

Paul Hoareau

Master's Research - Polytechnique Montréal

paul.hoareau@mila.quebec

youssef.laatar@mila.quebec

Youssef Laatar

Master's Research - Polytechnique Montréal

nathan.molinier@mila.quebec

Nathan Molinier

PhD - Polytechnique Montréal

Publications

Microscopy-BIDS: An Extension to the Brain Imaging Data Structure for Microscopy Data

Marie-Hélène Bourget

Lee Kamentsky

Satrajit S. Ghosh

Giacomo Mazzamuto

Alberto Lazari

Christopher J. Markiewicz

Robert Oostenveld

Guiomar Niso

Yaroslav O. Halchenko

Ilona Lipp

Sylvain Takerkart

Paule-Joanne Toussaint

Ali R. Khan

Gustav Nilsonne

Filippo Maria Castelli

Stefan Ross Eric Franklin Anthony Rémi Christopher J. Taylor Appelhoff

The Brain Imaging Data Structure (BIDS) is a specification for organizing, sharing, and archiving neuroimaging data and metadata in a reusab… (see more)le way. First developed for magnetic resonance imaging (MRI) datasets, the community-led specification evolved rapidly to include other modalities such as magnetoencephalography, positron emission tomography, and quantitative MRI (qMRI). In this work, we present an extension to BIDS for microscopy imaging data, along with example datasets. Microscopy-BIDS supports common imaging methods, including 2D/3D, ex/in vivo, micro-CT, and optical and electron microscopy. Microscopy-BIDS also includes comprehensible metadata definitions for hardware, image acquisition, and sample properties. This extension will facilitate future harmonization efforts in the context of multi-modal, multi-scale imaging such as the characterization of tissue microstructure with qMRI.

2022-04-18

Frontiers in Neuroscience (published)

Rapid, automated nerve histomorphometry through open-source artificial intelligence

Simeon Christian Daeschler

Marie-Hélène Bourget

Dorsa Derakhshan

Vasudev Sharma

Stoyan Ivaylov Asenov

Tessa Gordon

Gregory Howard Borschel

We aimed to develop and validate a deep learning model for automated segmentation and histomorphometry of myelinated peripheral nerve fibers… (see more) from light microscopic images. A convolutional neural network integrated in the AxonDeepSeg framework was trained for automated axon/myelin segmentation using a dataset of light-microscopic cross-sectional images of osmium tetroxide-stained rat nerves including various axonal regeneration stages. In a second dataset, accuracy of automated segmentation was determined against manual axon/myelin labels. Automated morphometry results, including axon diameter, myelin sheath thickness and g-ratio were compared against manual straight-line measurements and morphometrics extracted from manual labels with AxonDeepSeg as a reference standard. The neural network achieved high pixel-wise accuracy for nerve fiber segmentations with a mean (± standard deviation) ground truth overlap of 0.93 (± 0.03) for axons and 0.99 (± 0.01) for myelin sheaths, respectively. Nerve fibers were identified with a sensitivity of 0.99 and a precision of 0.97. For each nerve fiber, the myelin thickness, axon diameter, g-ratio, solidity, eccentricity, orientation, and individual x -and y-coordinates were determined automatically. Compared to manual morphometry, automated histomorphometry showed superior agreement with the reference standard while reducing the analysis time to below 2.5% of the time needed for manual morphometry. This open-source convolutional neural network provides rapid and accurate morphometry of entire peripheral nerve cross-sections. Given its easy applicability, it could contribute to significant time savings in biomedical research while extracting unprecedented amounts of objective morphologic information from large image datasets.

2022-04-07

Scientific Reports (published)

Comparison of multi-center MRI protocols for visualizing the spinal cord gray matter

Eva Alonso-Ortiz

Stephanie Alley

Maria Marcella Laganà

Francesca Baglio

Signe Johanna Vannesjo

Haleh Karbasforoushan

Maryam Seif

Alan C. Seifert

Junqian Xu

Joo-Won Kim

René Labounek

Lubomír Vojtíšek

Marek Dostál

Jan Valosek

Rebecca S. Samson

Francesco Grussu

Marco Battiston

Claudia A. M. Gandini Wheeler-Kingshott

Marios C. Yiannakas … (see 4 more)

Guillaume Gilbert

Torben Schneider

Brian Johnson

Ferrán Prados

We propose quality assessment criteria and metrics for gray‐matter visualization and apply them to different protocols. The proposed crite… (see more)ria and metrics, the analyzed protocols, and our open‐source code can serve as a benchmark for future optimization of spinal cord gray‐matter imaging protocols.

2022-04-04

Magnetic Resonance in Medicine (unknown)

Reproducibility and Evolution of Diffusion Mri Measurements Within the Cervical Spinal Cord in Multiple Sclerosis

Haykel Snoussi

Emmanuel Caruyer

Benoit Combes

Olivier Commowick

Élise Bannier

Anne Kerbrat

Christian Barillot

In Multiple Sclerosis (MS), there is a large discrepancy between the clinical observations and how the pathology is exhibited on brain image… (see more)s, this is known as the clinical-radiological paradox. One of the hypotheses is that the clinical deficit may be more related to the spinal cord damage than the number or location of lesions in the brain. Therefore, investigating how the spinal cord is damaged becomes an acute challenge to better understand and overcome this paradox. Diffusion MRI is known to provide quantitative figures of neuronal degeneration and axonal loss, in the brain as well as in the spinal cord. In this paper, we propose to investigate how diffusion MRI metrics vary in the different cervical regions with the progression of the disease. We first study the reproducibility of diffusion MRI on healthy volunteers with a test-retest procedure using both standard diffusion tensor imaging (DTI) and multi-compartment Ball-and-Stick models. Then, based on the test re-test quantitative calibration, we provide quantitative figures of pathology evolution between M0 and M12 in the cervical spine on a set of 31 MS patients, exhibiting how the pathology damage spans in the cervical spinal cord.

2022-03-27

2022 IEEE 19th International Symposium on Biomedical Imaging (ISBI) (published)

arxiv.org

Medical Image Segmentation on MRI Images with Missing Modalities: A Review

Reza Azad

Nika Khosravi

Mohammad Dehghanmanshadi

Dorit Merhof

2022-03-10

ArXiv (preprint)

arxiv.org

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… (see more)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 (published)

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… (see more) 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 (published)

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 (published)

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 (published)

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… (see more)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

(published)

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… (see more)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 (unknown)

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… (see more)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 (published)