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

Multi‐center benchmarking of cervical spinal cord RF coils for 7 T MRI: A traveling spines study

Eva Alonso‐Ortiz

Daniel Papp

Robert L. Barry

Kyota Poëti

Alan C. Seifert

Kyle M. Gilbert

Nibardo Lopez‐Rios

Jan Paska

Falk Eippert

Nikolaus Weiskopf

Laura Beghini

Nadine N. Graedel

Robert Trampel

Martina F. Callaghan

Christoph S. Aigner

Patrick Freund

Maryam Seif

Aurélien Destruel

Virginie Callot

Johanna Vannesjo … (see 1 more)

Julien Cohen‐Adad

The depth within the body, small diameter, long length, and varying tissue surrounding the spinal cord impose specific considerations when d… (see more)esigning RF coils. The optimal coil configuration for 7 T cervical spinal cord MRI is unknown and currently there are very few coil options. The purpose of this work was (1) to establish a quality control protocol for evaluating 7 T cervical spinal cord coils, and (2) to use that protocol to evaluate the performance of four different coil designs. Three healthy volunteers and a custom anthropomorphic phantom (the traveling spines cohort) were scanned at seven 7 T imaging centers using a common protocol and each center's specific cervical spinal cord coil. Four different coil designs were tested (two in‐house, one Rapid Biomedical, and one MRI.TOOLS design). The Rapid Biomedical coil was found to have the highest B1+ efficiency, whereas one of the in‐house designs (NeuroPoly Lab) had the highest SNR and the largest spinal cord coverage. The MRI.TOOLS coil had the most uniform B1+ profile along the cervical spinal cord; however, it was limited in its ability to provide the requested flip angles (especially for larger individuals). The latter was also the case for the second in‐house coil (MSSM). The results of this study serve as a guide for the spinal cord MRI community in selecting the most suitable coil based on specific requirements and offer a standardized protocol for assessing future coils.

2025-05-19

Magnetic Resonance in Medicine (published)

Influence of scanning plane on Human Spinal Cord functional Magnetic Resonance echo planar imaging

Marta Moraschi

Silvia Tommasin

Laura Maugeri

Mauro DiNuzzo

Marco Masullo

Fabio Mangini

Lorenzo Giovannelli

Daniele Mascali

Tommaso Gili

Valerio Pisani

Ugo Nocentini

Federico Giove

Michela Fratini

BACKGROUND: Functional Magnetic Resonance Imaging (fMRI) is based on the Blood Oxygenation Level Dependent contrast and has been exploited f… (see more)or the indirect study of the neuronal activity within both the brain and the spinal cord. However, the interpretation of spinal cord fMRI (scfMRI) is still controversial and its diffusion is rather limited because of technical limitations. Overcoming these limitations would have a beneficial effect for the assessment and follow-up of spinal injuries and neurodegenerative diseases. PURPOSE: This study was aimed at systematically verify whether sagittal scanning in scfMRI using EPI readout is a viable alternative to the more common axial scanning, and at optimizing a pipeline for EPI-based scfMRI data analysis, based on Spinal Cord Toolbox (SCT). METHODS: Forty-five healthy subjects underwent MRI acquisition in a Philips Achieva 3T MRI scanner. T2*-weighted fMRI data were acquired using a GE-EPI sequence along sagittal and axial planes during an isometric motor task. Differences on benchmarks were assessed via paired two-sample t-test at p=0.05. RESULTS: We investigated the impact of the acquisition strategy by means of various metrics such as Temporal Signal to Noise Ratio (tSNR), Dice Coefficient to assess geometric distortions, Reproducibility and Sensitivity. tSNR was higher in axial than in sagittal scans, as well as reproducibility within the whole cord mask (t=7.4, p0.01) and within the GM mask (t=4.2, p0.01). The other benchmarks, associated with distortion and functional response, showed no differenc

2025-05-11

PLOS One (published)

Impact of through‐slice gradient optimization for dynamic slice‐wise shimming in the cervico‐thoracic spinal cord

Arnaud Breheret

Alexandre D'Astous

Yixin Ma

Jason P. Stockmann

Julien Cohen‐Adad

This study investigates the effectiveness of through‐slice gradient optimization in dynamic slice‐wise B0 shimming of the cervico‐thor… (see more)acic spinal cord to enhance signal recovery in gradient‐echo (GRE) EPI sequences commonly used in functional MRI studies. Six volunteers underwent MRI acquisitions with dynamic shim updating (DSU) using a custom‐built 15‐channel AC/DC coil at 3 T. A magnetization‐prepared rapid gradient echo was acquired to segment the spine and to provide a clear image of the anatomical region of interest in the figures. GRE B0 field maps were used to measure field homogeneity before and after shimming; the pre‐shimming field map was used for optimization. Shimmed fields were dynamically applied to GRE–echo planar imaging acquisitions simulating functional MRI acquisitions under two shimming conditions: DSU with and without through‐slice gradient consideration. DSU with through‐slice gradient optimization increased the temporal signal‐to‐noise ratio at the T2 vertebral level by 201% compared with volume‐wise shim and by 28% compared with DSU without through‐slice. The residual geometric distortions were similar between DSU with and without through‐slice gradient optimization. A high signal loss penalty parameter was effective in simulations for reducing through‐slice gradient‐induced signal loss but led to instability and reduced image quality in actual acquisitions due to excessive in‐plane B0 inhomogeneities. Introducing a carefully balanced through‐slice gradient parameter in slice‐wise shimming substantially improves signal recovery in axial GRE images of the spinal cord, without compromising in‐plane homogeneity. This effective approach can advance spinal cord functional MRI applications at high field strengths.

2025-04-30

Magnetic Resonance in Medicine (published)

Spinal Cord Tract Integrity in Degenerative Cervical Myelopathy

Newton Cho

Abdul Al-Shawwa

W. Bradley Jacobs

Nathan Evaniew

Jacques Bouchard

Steve Casha

Stephan duPlessis

Peter Lewkonia

Fred Nicholls

Alex Soroceanu

Ganesh Swamy

Kenneth C. Thomas

Michael M. H. Yang

David W. Cadotte

Degenerative cervical myelopathy (DCM) is the most common cause of spinal dysfunction globally. Despite surgical intervention, motor dysfunc… (see more)tion may persist in many patients. The purpose of this study was to comprehensively examine specific spinal cord tract changes in patients with DCM, to better understand potential substrates for compensatory recovery of function. Cervical spinal cord MRI scans with diffusion tensor imaging were performed in patients with DCM and in healthy volunteers. Spinal Cord Toolbox was used to register the PAM50 template, which includes a probabilistic atlas of the white matter tracts of the spinal cord, to the imaging data. Fractional anisotropy (FA) was extracted for each tract at C3 above the level of maximal compression and compared between patients with DCM and healthy volunteers and between patients with mild vs moderate to severe DCM. We included 25 patients with DCM (13 mild and 12 moderate to severe) and 6 healthy volunteers. FA was significantly reduced in DCM subjects relative to healthy volunteers for the lateral corticospinal tract (mild DCM vs healthy ∆ = −0.13, P = .018; moderate to severe DCM vs healthy ∆ = −0.11, P = .047), fasciculus gracilis (mild DCM vs healthy ∆ = −0.16, P = .010; moderate to severe DCM vs healthy ∆ = −0.13, P = .039), and fasciculus cuneatus (mild DCM vs healthy ∆ = −0.16, P = .007; moderate to severe DCM vs healthy ∆ = −0.15, P = .012). There were no differences in FA for all tracts between mild and moderate-to-severe DCM subjects. Patients with DCM had altered diffusion tensor imaging signal in their lateral corticospinal tract, fasciculus gracilis, and fasciculus cuneatus in comparison with healthy volunteers. These findings indicate that DCM is characterized by injury to these structures, which suggests that other tracts within the cord could potentially act as substrates for compensatory motor recovery.

2025-04-02

Neurosurgery (unknown)

Addressing Missing Modality Challenges in MRI Images: A Comprehensive Review

Reza Azad

Mohammad Dehghanmanshadi

Nika Khosravi

Dorit Merhof

2025-03-31

Computational Visual Media (published)

Considerations and recommendations from the ISMRM Diffusion Study Group for preclinical diffusion MRI: Part 2 - Ex vivo imaging: added value and acquisition

Kurt G. Schilling

Francesco Grussu

Andrada Ianus

Brian Hansen

Amy F. D. Howard

Rachel L. C. Barrett

Manisha Aggarwal

Stijn Michielse

Fatima Nasrallah

Warda Syeda

Nian Wang

Jelle Veraart

Alard Roebroeck

Andrew F. Bagdasarian

Cornelius Eichner

Farshid Sepehrband

Jan Zimmermann

Lucas Soustelle

Christien Bowman

Benjamin C. Tendler … (see 38 more)

Andreea Hertanu

Ben Jeurissen

Marleen Verhoye

Lucio Frydman

Yohan van de Looij

David Hike

Jeff F. Dunn

Karla Miller

Bennett A. Landman

Noam Shemesh

Adam Anderson

Emilie McKinnon

Shawna Farquharson

Flavio Dell'Acqua

Carlo Pierpaoli

Ivana Drobnjak

Alexander Leemans

Kevin D. Harkins

Maxime Descoteaux

Duan Xu

Hao Huang

Mathieu D. Santin

Samuel C. Grant

Andre Obenaus

Gene S. Kim

Dan Wu

Denis Le Bihan

Stephen J. Blackband

Luisa Ciobanu

Els Fieremans

Ruiliang Bai

Trygve B. Leergaard

Jiangyang Zhang

Tim B. Dyrby

G. Allan Johnson

Julien Cohen‐Adad

Matthew D. Budde

Ileana O. Jelescu

The value of preclinical diffusion MRI (dMRI) is substantial. While dMRI enables in vivo non-invasive characterization of tissue, ex vivo dM… (see more)RI is increasingly used to probe tissue microstructure and brain connectivity. Ex vivo dMRI has several experimental advantages including higher signal-to-noise ratio and spatial resolution compared to in vivo studies, and enabling more advanced diffusion contrasts. Another major advantage of ex vivo dMRI is the direct comparison with histological data as a methodological validation. However, there are a number of considerations that must be made when performing ex vivo experiments. The steps from tissue preparation, image acquisition and processing, and interpretation of results are complex, with decisions that not only differ dramatically from in vivo imaging of small animals, but ultimately affect what questions can be answered using the data. This work represents "Part 2" of a 3-part series of recommendations and considerations for preclinical dMRI. We describe best practices for dMRI of ex vivo tissue, with a focus on the value that ex vivo imaging adds to the field of dMRI and considerations in ex vivo image acquisition. We give general considerations and foundational knowledge that must be considered when designing experiments. We describe differences in specimens and models and discuss why some may be more or less appropriate for different studies. We then give guidelines for ex vivo protocols, including tissue fixation, sample preparation, and MR scanning. In each section, we attempt to provide guidelines and recommendations, but also highlight areas for which no guidelines exist (and why), and where future work should lie. An overarching goal herein is to enhance the rigor and reproducibility of ex vivo dMRI acquisitions and analyses, and thereby advance biomedical knowledge.

2025-03-03

Magnetic Resonance in Medicine (published)

Normalizing Spinal Cord Compression Measures in Degenerative Cervical Myelopathy.

Sandrine Bédard

Jan Valosek

Maryam Seif

Armin Curt

Simon Schading-Sassenhausen

Nikolai Pfender

P. Freund

Markus Hupp

2025-02-28

The spine journal (published)

Considerations and recommendations from the <scp>ISMRM</scp> diffusion study group for preclinical diffusion <scp>MRI</scp>: Part 1: In vivo small‐animal imaging

Ileana O. Jelescu

Francesco Grussu

Andrada Ianus

Brian Hansen

Rachel L. C. Barrett

Manisha Aggarwal

Stijn Michielse

Fatima Nasrallah

Warda Syeda

Nian Wang

Jelle Veraart

Alard Roebroeck

Andrew F. Bagdasarian

Cornelius Eichner

Farshid Sepehrband

Jan Zimmermann

Lucas Soustelle

Christien Bowman

Benjamin C. Tendler

Andreea Hertanu … (see 37 more)

Ben Jeurissen

Marleen Verhoye

Lucio Frydman

Yohan van de Looij

David Hike

Jeff F. Dunn

Karla Miller

Bennett Landman

Noam Shemesh

Arthur Anderson

Emilie McKinnon

Shawna Farquharson

Flavio Dell’Acqua

Carlo Pierpaoli

Ivana Drobnjak

Alexander Leemans

Kevin D. Harkins

Maxime Descoteaux

Duan Xu

Hao Huang

Mathieu D. Santin

Samuel C. Grant

Andre Obenaus

Gene S. Kim

Dan Wu

Denis Le Bihan

Stephen J. Blackband

Luisa Ciobanu

Els Fieremans

Ruiliang Bai

Trygve B. Leergaard

Jiangyang Zhang

Tim B. Dyrby

G. Allan Johnson

Matthew D. Budde

Kurt G Schilling

2025-02-25

Magnetic Resonance in Medicine (published)

Considerations and recommendations from the ISMRM Diffusion Study Group for preclinical diffusion MRI: Part 3 -- Ex vivo imaging: data processing, comparisons with microscopy, and tractography

Kurt G Schilling

Amy F. D. Howard

Francesco Grussu

Andrada Ianus

Brian Hansen

Rachel L. C. Barrett

Manisha Aggarwal

Stijn Michielse

Fatima Nasrallah

Warda Syeda

Nian Wang

Jelle Veraart

Alard Roebroeck

Andrew F. Bagdasarian

Cornelius Eichner

Farshid Sepehrband

Jan Zimmermann

Lucas Soustelle

Christien Bowman

Benjamin C. Tendler … (see 38 more)

Andreea Hertanu

Ben Jeurissen

Marleen Verhoye

Lucio Frydman

Yohan van de Looij

David Hike

Jeff F. Dunn

Karla Miller

Bennett Landman

Noam Shemesh

Arthur Anderson

Emilie McKinnon

Shawna Farquharson

Flavio Dell’Acqua

Carlo Pierpaoli

Ivana Drobnjak

Alexander Leemans

Kevin D. Harkins

Maxime Descoteaux

Duan Xu

Hao Huang

Mathieu D. Santin

Samuel C. Grant

Andre Obenaus

Gene S. Kim

Dan Wu

Denis Le Bihan

Stephen J. Blackband

Luisa Ciobanu

Els Fieremans

Ruiliang Bai

Trygve B. Leergaard

Jiangyang Zhang

Tim B. Dyrby

G. Allan Johnson

Matthew D. Budde

Ileana O. Jelescu

2025-02-25

Magnetic Resonance in Medicine (published)

Recommendations and guidelines from the ISMRM Diffusion Study Group for preclinical diffusion MRI: Part 1 -- In vivo small-animal imaging

Ileana O. Jelescu

Francesco Grussu

Andrada Ianus

Brian Hansen

Rachel L. C. Barrett

Manisha Aggarwal

Stijn Michielse

Fatima Nasrallah

Warda Syeda

Nian Wang

Jelle Veraart

Alard Roebroeck

Andrew F. Bagdasarian

Cornelius Eichner

Farshid Sepehrband

Jan Zimmermann

Lucas Soustelle

Christien Bowman

Benjamin C. Tendler

Andreea Hertanu … (see 37 more)

Ben Jeurissen

Marleen Verhoye

Lucio Frydman

Yohan van de Looij

David Hike

Jeff F. Dunn

Karla Miller

Bennett A. Landman

Noam Shemesh

Adam Anderson

Emilie McKinnon

Shawna Farquharson

Flavio Dell'Acqua

Carlo Pierpaoli

Ivana Drobnjak

Alexander Leemans

Kevin D. Harkins

Maxime Descoteaux

Duan Xu

Hao Huang

Mathieu D. Santin

Samuel C. Grant

Andre Obenaus

Gene S. Kim

Dan Wu

Denis Le Bihan

Stephen J. Blackband

Luisa Ciobanu

Els Fieremans

Ruiliang Bai

Trygve B. Leergaard

Jiangyang Zhang

Tim B. Dyrby

G. Allan Johnson

Julien Cohen‐Adad

Matthew D. Budde

Kurt G. Schilling

The value of in vivo preclinical diffusion MRI (dMRI) is substantial. Small-animal dMRI has been used for methodological development and val… (see more)idation, characterizing the biological basis of diffusion phenomena, and comparative anatomy. Many of the influential works in this field were first performed in small animals or ex vivo samples. The steps from animal setup and monitoring, to acquisition, analysis, and interpretation are complex, with many decisions that may ultimately affect what questions can be answered using the data. This work aims to serve as a reference, presenting selected recommendations and guidelines from the diffusion community, on best practices for preclinical dMRI of in vivo animals. In each section, we also highlight areas for which no guidelines exist (and why), and where future work should focus. We first describe the value that small animal imaging adds to the field of dMRI, followed by general considerations and foundational knowledge that must be considered when designing experiments. We briefly describe differences in animal species and disease models and discuss how they are appropriate for different studies. We then give guidelines for in vivo acquisition protocols, including decisions on hardware, animal preparation, imaging sequences and data processing, including pre-processing, model-fitting, and tractography. Finally, we provide an online resource which lists publicly available preclinical dMRI datasets and software packages, to promote responsible and reproducible research. An overarching goal herein is to enhance the rigor and reproducibility of small animal dMRI acquisitions and analyses, and thereby advance biomedical knowledge.

2025-02-25

Magnetic Resonance in Medicine (published)

SCIsegV2: A Universal Tool for Segmentation of Intramedullary Lesions in Spinal Cord Injury

Enamundram Naga Karthik

Jan Valosek

Lynn Farner

Dario Pfyffer

Simon Schading-Sassenhausen

Anna Lebret

Gergely David

Andrew C. Smith

Kenneth A. Weber

Maryam Seif

Rhscir Network Imaging Group

Patrick Freund

2025-02-07

Lecture Notes in Computer Science (published)

Automatic segmentation of spinal cord lesions in MS: A robust tool for axial T2-weighted MRI scans

Enamundram Naga Karthik

Julian McGinnis

Ricarda Wurm

Sebastian Ruehling

Robert Graf

Jan Valosek

Pierre-Louis Benveniste

Markus Lauerer

Jason Talbott

Rohit Bakshi

Shahamat Tauhid

Timothy Shepherd

Achim Berthele

Claus Zimmer

Bernhard Hemmer

Daniel Rueckert

Benedikt Wiestler

Jan S. Kirschke

Mark Mühlau

Deep learning models have achieved remarkable success in segmenting brain white matter lesions in multiple sclerosis (MS), becoming integral… (see more) to both research and clinical workflows. While brain lesions have gained significant attention in MS research, the involvement of spinal cord lesions in MS is relatively understudied. This is largely owed to the variability in spinal cord magnetic resonance imaging (MRI) acquisition protocols, high individual anatomical differences, the complex morphology and size of spinal cord lesions - and lastly, the scarcity of labeled datasets required to develop robust segmentation tools. As a result, automatic segmentation of spinal cord MS lesions remains a significant challenge. Although some segmentation tools exist for spinal cord lesions, most have been developed using sagittal T2-weighted (T2w) sequences primarily focusing on cervical spines. With the growing importance of spinal cord imaging in MS, axial T2w scans are becoming increasingly relevant due to their superior sensitivity in detecting lesions compared to sagittal acquisition protocols. However, most existing segmentation methods struggle to effectively generalize to axial sequences due to differences in image characteristics caused by the highly anisotropic spinal cord scans. To address these challenges, we developed a robust, open-source lesion segmentation tool tailored specifically for axial T2w scans covering the whole spinal cord. We investigated key factors influencing lesion segmentation, including the impact of stitching together individually acquired spinal regions, straightening the spinal cord, and comparing the effectiveness of 2D and 3D convolutional neural networks (CNNs). Drawing on these insights, we trained a multi-center model using an extensive dataset of 582 MS patients, resulting in a dataset comprising an entirety of 2,167 scans. We empirically evaluated the model’s segmentation performance across various spinal segments for lesions with varying sizes. Our model significantly outperforms the current state-of-the-art methods, providing consistent segmentation across cervical, thoracic and lumbar regions. To support the broader research community, we integrate our model into the widely-used Spinal Cord Toolbox (v7.0 and above), making it accessible via the command sct_deepseg lesion_ms_axial_t2 -i <path-to-image.nii.gz>.

2024-12-31

Imaging Neuroscience (published)