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Jan Valosek

Postdoctorate - Polytechnique Montréal
Supervisor
Julien Cohen-Adad
Research Topics
Deep Learning
Medical Machine Learning
Website
Google Scholar
GitHub

Publications

SCIseg: Automatic Segmentation of T2-weighted Intramedullary Lesions in Spinal Cord Injury
Enamundram Naga Karthik
Jan Valosek
Andrew C. Smith
Dario Pfyffer
Simon Schading-Sassenhausen
Lynn Farner
Kenneth A. Weber
Patrick Freund
Julien Cohen-Adad
Background: Quantitative MRI biomarkers in spinal cord injury (SCI) can help understand the extent of the focal injury. However, due to the … (see more)lack of automatic segmentation methods, these biomarkers are derived manually, which is a time-consuming process prone to intra- and inter-rater variability, thus limiting large multi-site studies and translation to clinical workflows. Purpose: To develop a deep learning tool for the automatic segmentation of T2-weighted hyperintense lesions and the spinal cord in SCI patients. Material and Methods: This retrospective study included a cohort of SCI patients from three sites enrolled between July 2002 and February 2023 who underwent clinical MRI examination. A deep learning model, SCIseg, was trained on T2-weighted images with heterogeneous image resolutions (isotropic, anisotropic), and orientations (axial, sagittal) acquired using scanners from different manufacturers (Siemens, Philips, GE) and different field strengths (1T, 1.5T, 3T) for the automatic segmentation of SCI lesions and the spinal cord. The proposed method was visually and quantitatively compared with other open-source baseline methods. Quantitative biomarkers (lesion volume, lesion length, and maximal axial damage ratio) computed from manual ground-truth lesion masks and automatic SCIseg predictions were correlated with clinical scores (pinprick, light touch, and lower extremity motor scores). A between-group comparison was performed using the Wilcoxon signed-rank test. Results: MRI data from 191 SCI patients (mean age, 48.1 years {+/-} 17.9 [SD]; 142 males) were used for training. Compared to existing methods, SCIseg achieved the best segmentation performance for both the cord and lesions and generalized well to both traumatic and non-traumatic SCI patients. SCIseg is open-source and accessible through the Spinal Cord Toolbox. Conclusion: Automatic segmentation of intramedullary lesions commonly seen in traumatic SCI replaces the tedious manual annotation process and enables the extraction of relevant lesion morphometrics in large cohorts. The proposed model generalizes across lesion etiologies (traumatic, ischemic), scanner manufacturers and heterogeneous image resolutions.
2024-01-03
medRxiv (preprint)
doi.org
Reproducible Spinal Cord Quantitative MRI Analysis with the Spinal Cord Toolbox.
Jan Valosek
Julien Cohen-Adad
2024-01-01
Magnetic Resonance in Medical Sciences (published)
doi.org
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
Julien Cohen-Adad
2024-01-01
AMAI@MICCAI (published)
doi.org
arxiv.org
Comparison of multicenter MRI protocols for visualizing the spinal cord gray matter
Julien Cohen-Adad
Eva Alonso‐Ortiz
Stephanie Alley
Maria Marcella Lagana
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
Ferran Prados
Spinal cord gray‐matter imaging is valuable for a number of applications, but remains challenging. The purpose of this work was to compare… (see more) various MRI protocols at 1.5 T, 3 T, and 7 T for visualizing the gray matter.
2022-04-05
Magnetic Resonance in Medicine (published)
doi.org
Comparison of multicenter MRI protocols for visualizing the spinal cord gray matter
Julien Cohen-Adad
Eva Alonso‐Ortiz
Stephanie Alley
M. M. Laganá
Francesca Baglio
S. Vannesjo
Haleh Karbasforoushan
Maryam Seif
A. Seifert
Junqian Xu
Joo-won Kim
René Labounek
Lubomír Vojtíšek
Marek Dostál
Jan Valosek
Rebecca Sara Samson
Francesco Grussu
Marco Battiston
C. G. Gandini Wheeler-Kingshott
Marios C. Yiannakas … (see 4 more)
Guillaume Gilbert
Torben Schneider
Brian Johnson
Ferran Prados
Spinal cord gray‐matter imaging is valuable for a number of applications, but remains challenging. The purpose of this work was to compare… (see more) various MRI protocols at 1.5 T, 3 T, and 7 T for visualizing the gray matter.
2022-04-05
Magnetic Resonance in Medicine (published)
doi.org
Comparison of multicenter MRI protocols for visualizing the spinal cord gray matter
Julien Cohen-Adad
Eva Alonso‐Ortiz
Stephanie Alley
Maria Marcella Lagana
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
Ferran Prados
Spinal cord gray‐matter imaging is valuable for a number of applications, but remains challenging. The purpose of this work was to compare… (see more) various MRI protocols at 1.5 T, 3 T, and 7 T for visualizing the gray matter.
2022-04-05
Magnetic Resonance in Medicine (published)
doi.org
Author Correction: Open-access quantitative MRI data of the spinal cord and reproducibility across participants, sites and manufacturers
Julien Cohen-Adad
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 … (see 71 more)
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 Lagana
Cornelia Laule
Christine S. Law
Christophe Lenglet
Tobias Leutritz
Yaou Liu
Sara Llufriu
Sean Mackey
Eloy Martinez-Heras
Loan Mattera
Igor Nestrašil
Kristin P. O’Grady
Nico Papinutto
Daniel Papp
Deborah Pareto
Todd B. Parrish
Anna Pichiecchio
Ferran 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
2021-09-23
Scientific Data (published)
doi.org
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 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 … (see 71 more)
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 Lagana
Cornelia Laule
Christine S. Law
Christophe Lenglet
Tobias Leutritz
Yaou Liu
Sara Llufriu
Sean Mackey
Eloy Martinez-Heras
Loan Mattera
Igor Nestrašil
Kristin P. O’Grady
Nico Papinutto
Daniel Papp
Deborah Pareto
Todd B. Parrish
Anna Pichiecchio
Ferran 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 C. Yiannakas
K. Weber
Nikolaus Weiskopf
Richard G. Wise
Patrik O. Wyss
Junqian Xu
2021-08-16
Nature Protocols (published)
doi.org
Open-access quantitative MRI data of the spinal cord and reproducibility across participants, sites and manufacturers
Julien Cohen-Adad
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 … (see 71 more)
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 Lagana
Cornelia Laule
Christine S. Law
Christophe Lenglet
Tobias Leutritz
Yaou Liu
Sara Llufriu
Sean Mackey
Eloy Martinez-Heras
Loan Mattera
Igor Nestrašil
Kristin P. O’Grady
Nico Papinutto
Daniel Papp
Deborah Pareto
Todd B. Parrish
Anna Pichiecchio
Ferran 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
2021-08-16
Scientific Data (published)
doi.org
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 Hluštík
Eva Vlčková
Zdeněk Kadaňka
Josef Bednařík
Alena Svatkova
Non‐myelopathic degenerative cervical spinal cord compression (NMDC) frequently occurs throughout aging and may progress to potentially ir… (see more)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.
2021-07-21
European Journal of Neurology (published)
doi.org