Julien Cohen-Adad

SCIseg: Automatic Segmentation of Intramedullary Lesions in Spinal Cord Injury on T2-weighted MRI Scans.

Enamundram Naga Karthik

Jan Valošek

Andrew C. Smith

Dario Pfyffer

Simon Schading-Sassenhausen

Lynn Farner

KA Weber

Kenneth A. Weber

Patrick Freund

Julien Cohen-Adad

"Just Accepted" papers have undergone full peer review and have been accepted for publication in Radiology: Artificial Intelligence. This ar… (voir plus)ticle will undergo copyediting, layout, and proof review before it is published in its final version. Please note that during production of the final copyedited article, errors may be discovered which could affect the content. Purpose To develop a deep learning tool for the automatic segmentation of the spinal cord and intramedullary lesions in spinal cord injury (SCI) on T2-weighted MRI scans. Materials and Methods This retrospective study included MRI data acquired between July 2002 and February 2023 from 191 patients with SCI (mean age, 48.1 years ± 17.9 [SD]; 142 males). The data consisted of T2-weighted MRI acquired using different scanner manufacturers with various image resolutions (isotropic and anisotropic) and orientations (axial and sagittal). Patients had different lesion etiologies (traumatic, ischemic, and hemorrhagic) and lesion locations across the cervical, thoracic and lumbar spine. A deep learning model, SCIseg, was trained in a three-phase process involving active learning for the automatic segmentation of intramedullary SCI lesions and the spinal cord. The segmentations from the proposed model were visually and quantitatively compared with those from three other open-source methods (PropSeg, DeepSeg and contrast-agnostic, all part of the Spinal Cord Toolbox). Wilcoxon signed-rank test was used to compare quantitative MRI biomarkers of SCI (lesion volume, lesion length, and maximal axial damage ratio) derived from the manual reference standard lesion masks and biomarkers obtained automatically with SCIseg segmentations. Results SCIseg achieved a Dice score of 0.92 ± 0.07 (mean ± SD) and 0.61 ± 0.27 for spinal cord and SCI lesion segmentation, respectively. There was no evidence of a difference between lesion length (P = .42) and maximal axial damage ratio (P = .16) computed from manually annotated lesions and the lesion segmentations obtained using SCIseg. Conclusion SCIseg accurately segmented intramedullary lesions on a diverse dataset of T2-weighted MRI scans and extracted relevant lesion biomarkers (namely, lesion volume, lesion length, and maximal axial damage ratio). SCIseg is open-source and accessible through the Spinal Cord Toolbox (v6.2 and above). Published under a CC BY 4.0 license.

2024-11-06

Radiology: Artificial Intelligence (publié)

doi.org

SCIseg: Automatic Segmentation of Intramedullary Lesions in Spinal Cord Injury on T2-weighted MRI Scans.

Enamundram Naga Karthik

Jan Valošek

Andrew C. Smith

Dario Pfyffer

Simon Schading-Sassenhausen

Lynn Farner

KA Weber

Patrick Freund

Julien Cohen-Adad

"Just Accepted" papers have undergone full peer review and have been accepted for publication in Radiology: Artificial Intelligence. This ar… (voir plus)ticle will undergo copyediting, layout, and proof review before it is published in its final version. Please note that during production of the final copyedited article, errors may be discovered which could affect the content. Purpose To develop a deep learning tool for the automatic segmentation of the spinal cord and intramedullary lesions in spinal cord injury (SCI) on T2-weighted MRI scans. Materials and Methods This retrospective study included MRI data acquired between July 2002 and February 2023 from 191 patients with SCI (mean age, 48.1 years ± 17.9 [SD]; 142 males). The data consisted of T2-weighted MRI acquired using different scanner manufacturers with various image resolutions (isotropic and anisotropic) and orientations (axial and sagittal). Patients had different lesion etiologies (traumatic, ischemic, and hemorrhagic) and lesion locations across the cervical, thoracic and lumbar spine. A deep learning model, SCIseg, was trained in a three-phase process involving active learning for the automatic segmentation of intramedullary SCI lesions and the spinal cord. The segmentations from the proposed model were visually and quantitatively compared with those from three other open-source methods (PropSeg, DeepSeg and contrast-agnostic, all part of the Spinal Cord Toolbox). Wilcoxon signed-rank test was used to compare quantitative MRI biomarkers of SCI (lesion volume, lesion length, and maximal axial damage ratio) derived from the manual reference standard lesion masks and biomarkers obtained automatically with SCIseg segmentations. Results SCIseg achieved a Dice score of 0.92 ± 0.07 (mean ± SD) and 0.61 ± 0.27 for spinal cord and SCI lesion segmentation, respectively. There was no evidence of a difference between lesion length (P = .42) and maximal axial damage ratio (P = .16) computed from manually annotated lesions and the lesion segmentations obtained using SCIseg. Conclusion SCIseg accurately segmented intramedullary lesions on a diverse dataset of T2-weighted MRI scans and extracted relevant lesion biomarkers (namely, lesion volume, lesion length, and maximal axial damage ratio). SCIseg is open-source and accessible through the Spinal Cord Toolbox (v6.2 and above). Published under a CC BY 4.0 license.

2024-11-06

Radiology: Artificial Intelligence (publié)

doi.org

Spinal cord evaluation in multiple sclerosis: clinical and radiological associations, present and future

B Mark Keegan

Martina Absinta

Julien Cohen-Adad

Eoin P Flanagan

Roland G Henry

Eric C Klawiter

Shannon Kolind

Stephen Krieger

Cornelia Laule

John A Lincoln

Steven Messina

Jiwon Oh

Nico Papinutto

Seth Aaron Smith

Anthony Traboulsee

2024-11-06

Brain Communications (publié)

doi.org

Spinal cord evaluation in multiple sclerosis: clinical and radiological associations, present and future

B Mark Keegan

Martina Absinta

Julien Cohen-Adad

Eoin P Flanagan

Roland G Henry

Eric C Klawiter

Shannon Kolind

Stephen Krieger

Cornelia Laule

John A Lincoln

Steven Messina

Jiwon Oh

Nico Papinutto

Seth Aaron Smith

Anthony Traboulsee

Abstract Spinal cord disease is important in most people with multiple sclerosis, but assessment remains less emphasized in patient care, ba… (voir plus)sic and clinical research and therapeutic trials. The North American Imaging in Multiple Sclerosis Spinal Cord Interest Group was formed to determine and present the contemporary landscape of multiple sclerosis spinal cord evaluation, further existing and advanced spinal cord imaging techniques, and foster collaborative work. Important themes arose: (i) multiple sclerosis spinal cord lesions (differential diagnosis, association with clinical course); (ii) spinal cord radiological–pathological associations; (iii) ‘critical’ spinal cord lesions; (iv) multiple sclerosis topographical model; (v) spinal cord atrophy; and (vi) automated and special imaging techniques. Distinguishing multiple sclerosis from other myelopathic aetiology is increasingly refined by imaging and serological studies. Post-mortem spinal cord findings and MRI pathological correlative studies demonstrate MRI’s high sensitivity in detecting microstructural demyelination and axonal loss. Spinal leptomeninges include immune inflammatory infiltrates, some in B-cell lymphoid-like structures. ‘Critical’ demyelinating lesions along spinal cord corticospinal tracts are anatomically consistent with and may be disproportionately associated with motor progression. Multiple sclerosis topographical model implicates the spinal cord as an area where threshold impairment associates with multiple sclerosis disability. Progressive spinal cord atrophy and ‘silent’ multiple sclerosis progression may be emerging as an important multiple sclerosis prognostic biomarker. Manual atrophy assessment is complicated by rater bias, while automation (e.g. Spinal Cord Toolbox), and artificial intelligence may reduce this. Collaborative research by the North American Imaging in Multiple Sclerosis and similar groups with experts combining distinct strengths is key to advancing assessment and treatment of people with multiple sclerosis spinal cord disease.

2024-11-06

Brain Communications (publié)

doi.org

Spiral volumetric optoacoustic tomography of reduced oxygen saturation in the spinal cord of M83 mouse model of Parkinson's disease.

Benjamin F. Combes

Sandeep Kumar Kalva

Pierre-Louis Benveniste

Agathe Tournant

Man Hoi Law

Joshua Newton

Maik Krüger

Rebecca Z. Weber

Inês Dias

Daniela Noain

Xose Luis Dean-Ben

Uwe Konietzko

Christian R. Baumann

Per-Göran Gillberg

Christoph Hock

Roger M. Nitsch

Julien Cohen-Adad

Daniel Razansky

Ruiqing Ni

2024-10-09

European Journal of Nuclear Medicine and Molecular Imaging (publié)

doi.org

Spiral volumetric optoacoustic tomography of reduced oxygen saturation in the spinal cord of M83 mouse model of Parkinson’s disease

Benjamin F. Combes

Sandeep Kumar Kalva

Pierre-Louis Benveniste

Agathe Tournant

Man Hoi Law

Joshua Newton

Maik Krüger

Rebecca Z Weber

Inês Dias

Daniela Noain

Xose Luis Dean-Ben

Uwe Konietzko

Christian R. Baumann

Per-Göran Gillberg

Christoph Hock

Roger M. Nitsch

Julien Cohen-Adad

Daniel Razansky

Ruiqing Ni

2024-10-09

European Journal of Nuclear Medicine and Molecular Imaging (publié)

doi.org

RF shimming in the cervical spinal cord at 7 T.

Daniel Papp

Kyle M. Gilbert

Gaspard Cereza

Alexandre D'Astous

Nibardo Lopez‐Rios

Mathieu Boudreau

Marcus J. Couch

Pedram Yazdanbakhsh

Robert L. Barry

Eva Alonso‐Ortiz

Julien Cohen-Adad

PURPOSE Advancing the development of 7 T MRI for spinal cord imaging is crucial for the enhanced diagnosis and monitoring of various neurode… (voir plus)generative diseases and traumas. However, a significant challenge at this field strength is the transmit field inhomogeneity. Such inhomogeneity is particularly problematic for imaging the small, deep anatomical structures of the cervical spinal cord, as it can cause uneven signal intensity and elevate the local specific absorption ratio, compromising image quality. This multisite study explores several RF shimming techniques in the cervical spinal cord. METHODS Data were collected from 5 participants between two 7 T sites with a custom 8Tx/20Rx parallel transmission coil. We explored two radiofrequency (RF) shimming approaches from an MRI vendor and four from an open-source toolbox, showcasing their ability to enhance transmit field and signal homogeneity along the cervical spinal cord. RESULTS The circularly polarized (CP), coefficient of variation (CoV), and specific absorption rate (SAR) efficiency shim modes showed the highest B1 + efficiency, and the vendor-based "patient" and "volume" modes showed the lowest B1 + efficiency. The coefficient of variation method produced the highest CSF/spinal cord contrast on T2*-weighted scans (ratio of 1.27 ± 0.03), and the lowest variation of that contrast along the superior-inferior axis. CONCLUSION The study's findings highlight the potential of RF shimming to advance 7 T MRI's clinical utility for central nervous system imaging by enabling more homogenous and efficient spinal cord imaging. Additionally, the research incorporates a reproducible Jupyter Notebook, enhancing the study's transparency and facilitating peer verification.

2024-08-13

Magnetic Resonance in Medicine (publié)

doi.org

<scp>RF</scp> shimming in the cervical spinal cord at <scp>7 T</scp>

Daniel Papp

Kyle M. Gilbert

Gaspard Cereza

Alexandre D'Astous

Nibardo Lopez‐Rios

Mathieu Boudreau

Marcus J. Couch

Pedram Yazdanbakhsh

Robert L. Barry

Eva Alonso‐Ortiz

Julien Cohen-Adad

2024-08-13

Magnetic Resonance in Medicine (publié)

doi.org

RF shimming in the cervical spinal cord at 7 T.

Daniel Papp

Kyle M. Gilbert

Gaspard Cereza

Alexandre D'Astous

Nibardo Lopez‐Rios

Mathieu Boudreau

Marcus J. Couch

Pedram Yazdanbakhsh

Robert L. Barry

Eva Alonso‐Ortiz

Julien Cohen-Adad

PURPOSE Advancing the development of 7 T MRI for spinal cord imaging is crucial for the enhanced diagnosis and monitoring of various neurode… (voir plus)generative diseases and traumas. However, a significant challenge at this field strength is the transmit field inhomogeneity. Such inhomogeneity is particularly problematic for imaging the small, deep anatomical structures of the cervical spinal cord, as it can cause uneven signal intensity and elevate the local specific absorption ratio, compromising image quality. This multisite study explores several RF shimming techniques in the cervical spinal cord. METHODS Data were collected from 5 participants between two 7 T sites with a custom 8Tx/20Rx parallel transmission coil. We explored two radiofrequency (RF) shimming approaches from an MRI vendor and four from an open-source toolbox, showcasing their ability to enhance transmit field and signal homogeneity along the cervical spinal cord. RESULTS The circularly polarized (CP), coefficient of variation (CoV), and specific absorption rate (SAR) efficiency shim modes showed the highest B1 + efficiency, and the vendor-based "patient" and "volume" modes showed the lowest B1 + efficiency. The coefficient of variation method produced the highest CSF/spinal cord contrast on T2*-weighted scans (ratio of 1.27 ± 0.03), and the lowest variation of that contrast along the superior-inferior axis. CONCLUSION The study's findings highlight the potential of RF shimming to advance 7 T MRI's clinical utility for central nervous system imaging by enabling more homogenous and efficient spinal cord imaging. Additionally, the research incorporates a reproducible Jupyter Notebook, enhancing the study's transparency and facilitating peer verification.

2024-08-13

Magnetic Resonance in Medicine (publié)

doi.org

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

Enamundram Naga Karthik

Jan Valošek

Lynn Farner

Dario Pfyffer

Simon Schading-Sassenhausen

A. Lebret

Gergely David

Andrew Smith

Kenneth A. Weber

Maryam Seif

Rhscir Network Imaging Group

Patrick Freund

Julien Cohen-Adad

Spinal cord injury (SCI) is a devastating incidence leading to permanent paralysis and loss of sensory-motor functions potentially resulting… (voir plus) in the formation of lesions within the spinal cord. Imaging biomarkers obtained from magnetic resonance imaging (MRI) scans can predict the functional recovery of individuals with SCI and help choose the optimal treatment strategy. Currently, most studies employ manual quantification of these MRI-derived biomarkers, which is a subjective and tedious task. In this work, we propose (i) a universal tool for the automatic segmentation of intramedullary SCI lesions, dubbed \texttt{SCIsegV2}, and (ii) a method to automatically compute the width of the tissue bridges from the segmented lesion. Tissue bridges represent the spared spinal tissue adjacent to the lesion, which is associated with functional recovery in SCI patients. The tool was trained and validated on a heterogeneous dataset from 7 sites comprising patients from different SCI phases (acute, sub-acute, and chronic) and etiologies (traumatic SCI, ischemic SCI, and degenerative cervical myelopathy). Tissue bridges quantified automatically did not significantly differ from those computed manually, suggesting that the proposed automatic tool can be used to derive relevant MRI biomarkers. \texttt{SCIsegV2} and the automatic tissue bridges computation are open-source and available in Spinal Cord Toolbox (v6.4 and above) via the \texttt{sct\_deepseg -task seg\_sc\_lesion\_t2w\_sci} and \texttt{sct\_analyze\_lesion} functions, respectively.

2024-07-24

ArXiv (prépublication)

doi.org

arxiv.org

Myelin basic protein mRNA levels affect myelin sheath dimensions, architecture, plasticity, and density of resident glial cells

Hooman Bagheri

Hana Friedman

Amanda Hadwen

Celia Jarweh

Ellis Cooper

Lawrence Oprea

Claire Guerrier

Anmar Khadra

Armand Collin

Julien Cohen-Adad

Amanda Young

Gerardo Mendez Victoriano

Matthew Swire

Andrew Jarjour

Marie E. Bechler

Rachel S. Pryce

Pierre Chaurand

Lise Cougnaud

Dajana Vuckovic

Elliott Wilion … (voir 11 de plus)

Owen Greene

Akiko Nishiyama

Anouk Benmamar‐Badel

Trevor Owens

Vladimir Grouza

Marius Tuznik

Hanwen Liu

David A. Rudko

Jinyi Zhang

Katherine A. Siminovitch

Alan C. Peterson

Abstract Myelin Basic Protein (MBP) is essential for both elaboration and maintenance of CNS myelin, and its reduced accumulation results in… (voir plus) hypomyelination. How different Mbp mRNA levels affect myelin dimensions across the lifespan and how resident glial cells may respond to such changes are unknown. Here, to investigate these questions, we used enhancer‐edited mouse lines that accumulate Mbp mRNA levels ranging from 8% to 160% of wild type. In young mice, reduced Mbp mRNA levels resulted in corresponding decreases in Mbp protein accumulation and myelin sheath thickness, confirming the previously demonstrated rate‐limiting role of Mbp transcription in the control of initial myelin synthesis. However, despite maintaining lower line specific Mbp mRNA levels into old age, both MBP protein levels and myelin thickness improved or fully normalized at rates defined by the relative Mbp mRNA level. Sheath length, in contrast, was affected only when mRNA levels were very low, demonstrating that sheath thickness and length are not equally coupled to Mbp mRNA level. Striking abnormalities in sheath structure also emerged with reduced mRNA levels. Unexpectedly, an increase in the density of all glial cell types arose in response to reduced Mbp mRNA levels. This investigation extends understanding of the role MBP plays in myelin sheath elaboration, architecture, and plasticity across the mouse lifespan and illuminates a novel axis of glial cell crosstalk.

2024-07-18

Glia (publié)

doi.org

Myelin basic protein mRNA levels affect myelin sheath dimensions, architecture, plasticity, and density of resident glial cells

Hooman Bagheri

Hana Friedman

Amanda Hadwen

Celia Jarweh

Ellis Cooper

Lawrence Oprea

Claire Guerrier

Anmar Khadra

Armand Collin

Julien Cohen-Adad

Amanda Young

Gerardo Mendez Victoriano

Matthew Swire

Andrew Jarjour

Marie E. Bechler

Rachel S. Pryce

Pierre Chaurand

Lise Cougnaud

Dajana Vuckovic

Elliott Wilion … (voir 11 de plus)

Owen Greene

Akiko Nishiyama

Anouk Benmamar‐Badel

Trevor Owens

Vladimir Grouza

Marius Tuznik

Hanwen Liu

David A. Rudko

Jinyi Zhang

Katherine A. Siminovitch

Alan C. Peterson

Abstract Myelin Basic Protein (MBP) is essential for both elaboration and maintenance of CNS myelin, and its reduced accumulation results in… (voir plus) hypomyelination. How different Mbp mRNA levels affect myelin dimensions across the lifespan and how resident glial cells may respond to such changes are unknown. Here, to investigate these questions, we used enhancer‐edited mouse lines that accumulate Mbp mRNA levels ranging from 8% to 160% of wild type. In young mice, reduced Mbp mRNA levels resulted in corresponding decreases in Mbp protein accumulation and myelin sheath thickness, confirming the previously demonstrated rate‐limiting role of Mbp transcription in the control of initial myelin synthesis. However, despite maintaining lower line specific Mbp mRNA levels into old age, both MBP protein levels and myelin thickness improved or fully normalized at rates defined by the relative Mbp mRNA level. Sheath length, in contrast, was affected only when mRNA levels were very low, demonstrating that sheath thickness and length are not equally coupled to Mbp mRNA level. Striking abnormalities in sheath structure also emerged with reduced mRNA levels. Unexpectedly, an increase in the density of all glial cell types arose in response to reduced Mbp mRNA levels. This investigation extends understanding of the role MBP plays in myelin sheath elaboration, architecture, and plasticity across the mouse lifespan and illuminates a novel axis of glial cell crosstalk.

2024-07-18

Glia (publié)

doi.org

À la hauteur du moment

Perspectives sur l’IA pour les responsables des politiques

Mila Techaide 2025

Développement du groupe d'experts de l'ONU sur l'IA

Transition à la direction scientifique de Mila

À la hauteur du moment

Perspectives sur l’IA pour les responsables des politiques

Julien Cohen-Adad

Biographie

Étudiants actuels

Publications

À la hauteur du moment

Perspectives sur l’IA pour les responsables des politiques

Mila Techaide 2025

Développement du groupe d'experts de l'ONU sur l'IA

Transition à la direction scientifique de Mila

À la hauteur du moment

Perspectives sur l’IA pour les responsables des politiques

Mots-clés populaires:

Julien Cohen-Adad

Biographie

Étudiants actuels

Publications