Jan Valosek

Kalum Ost

Maxime Bouthillier

Gergely Dávid

Maryam Seif

Armin Curt

Nikolai Pfender

Markus Hupp

Patrick Freund

Tomáš Horák

Petr Kudlička

Josef Bednařík

Fauziyya Muhammad

Zachary A. Smith

2026-01-31

European Journal of Radiology Artificial Intelligence (published)

Monitoring morphometric drift in lifelong learning segmentation of the spinal cord.

Enamundram Naga Karthik

Christoph Stefan Aigner

Elise Bannier

Josef Bednařík

Virginie Callot

Anna Combes

Armin Curt

Gergely Dávid

Falk Eippert

Lynn Farner

Michael G. Fehlings

Patrick Freund

Tobias Granberg

Cristina Granziera

RHSCIR Network Imaging Group

Ulrike Horn

Tomáš Horák

Suzanne Humphreys … (see 36 more)

Markus Hupp

Anne Kerbrat

Nawal Kinany

Shannon Kolind

Petr Kudlička

Anna Lebret

Lisa Eunyoung Lee

Cristina Granziera

Allan R. Martin

Govind Nair

Megan McGrath

Kristin P. O’Grady

Jiwon Oh

Russell Ouellette

Nikolai Pfender

Dario Pfyffer

Pierre‐François Pradat

Alexandre Prat

Daniel S. Reich

Ilaria Ricchi

Naama Rotem‐Kohavi

Simon Schading-Sassenhausen

Maryam Seif

Andrew Smith

Seth A. Smith

Grace Sweeney

Roger Tam

Anthony Traboulsee

Constantina A. Treaba

Charidimos Tsagkas

Dimitri Van De Ville

Zachary Vavasour

Kenneth A. Weber

Sarath Chandar

Morphometric measures derived from spinal cord segmentations can serve as diagnostic and prognostic biomarkers in neurological diseases and … (see more)injuries affecting the spinal cord. For instance, the spinal cord cross-sectional area can be used to monitor cord atrophy in multiple sclerosis and to characterize compression in degenerative cervical myelopathy. While robust, automatic segmentation methods to a wide variety of contrasts and pathologies have been developed over the past few years, whether their predictions are stable as the model is updated using new datasets has not been assessed. This is particularly important for deriving normative values from healthy participants. In this study, we present a spinal cord segmentation model trained on a multisite (n=75) dataset, including 9 different MRI contrasts and several spinal cord pathologies. We also introduce a lifelong learning framework to automatically monitor the morphometric drift as the model is updated using additional datasets. The framework is triggered by an automatic GitHub Actions workflow every time a new model is created, recording the morphometric values derived from the model's predictions over time. As a real-world application of the proposed framework, we employed the spinal cord segmentation model to update a recently-introduced normative database of healthy participants containing commonly used measures of spinal cord morphometry. Results showed that: (i) our model performs well compared to its previous versions and existing pathology-specific models on the lumbar spinal cord, images with severe compression, and in the presence of intramedullary lesions and/or atrophy achieving an average Dice score of 0.95 ± 0.03; (ii) the automatic workflow for monitoring morphometric drift provides a quick feedback loop for developing future segmentation models; and (iii) the scaling factor required to update the database of morphometric measures is nearly constant among slices across the given vertebral levels, showing minimum drift between the current and previous versions of the model monitored by the framework. The model is freely available in Spinal Cord Toolbox v7.0.

2026-01-21

Imaging neuroscience (published)

openreview.net

Building a library of acute traumatic spinal cord injury images across Canada: a retrospective cohort study protocol

Naama Rotem-Kohavi

Suzanne Humphreys

Vanessa K Noonan

Christiana L Cheng

Mathieu Guay-Paquet

Maxime Bouthillier

Enamundram Naga Karthik

Emma Lichtenstein

Nick Guenther

Kalum Ost

Naj Attabib

Michael Hardisty

Jetan Badhiwala

Jeremie Larouche

Markian Pahuta

Sean Christie

Michael G Fehlings

Daryl Fourney

Brian K Kwon … (see 6 more)

Jean Marc Mac-Thiong

Jérôme Paquet

Philippe Phan

Christopher Witiw

David W Cadotte

MRI is increasingly recognised as a valuable tool for assessing prognosis and predicting outcomes following traumatic spinal cord injury (SC… (see more)I). Several potential MRI biomarkers have been identified, but efforts are still needed to improve the accuracy and feasibility of these biomarkers in clinical practice. This study aims to build a national Canadian SCI imaging repository for storing and analysing imaging data for SCI, with the goal of improving SCI MRI biomarkers to predict outcomes and inform clinical management. As a substudy of the Rick Hansen SCI Registry (RHSCIR), this retrospective multisite study includes individuals who sustained a traumatic cervical SCI between 2015 and 2021, were previously enrolled in RHSCIR, and had MRI scans acquired within 72 hours of injury and before any surgical intervention. Individuals with a penetrating trauma and/or with any prior spine surgery are excluded. The study principal investigator and research associates, experienced with data curation and with the standardised format and specifications of the Brain Imaging Data Structure standard, guide the site’s curator on the steps to perform image deidentification and curation to create standardised datasets across all sites. These datasets are transferred to a Digital Research Alliance of Canada (‘the Alliance’) server designated for this project and concatenated to form the national Canadian SCI imaging repository (Neurogitea). We are using a semiautomated processing pipeline to quantify lesion morphology, together with additional imaging measures that are manually extracted from the images (for instance, the relative maximal spinal cord compression and the maximum canal compromise). Through linkage to RHSCIR clinical and epidemiological data already available on eligible participants, regression analysis is planned to predict neurological outcomes at discharge, including the American Spinal Injury Association Impairment Scale grade, upper and lower extremity motor and sensory scores. This protocol has been submitted by the participating sites to obtain ethics and institutional approvals prior to the study initiation at each site. All 12 sites across Canada have now obtained ethics and institutional approvals. Study results will be disseminated at local, national and international conferences and by journal publications.

2025-11-30

BMJ Open (published)

RootletSeg: Deep learning method for spinal rootlets segmentation across MRI contrasts

Katerina Krejci

Jiri Chmelik

Sandrine B'edard

Falk Eippert

Ulrike Horn

Virginie Callot

Purpose: To develop a deep learning method for the automatic segmentation of spinal nerve rootlets on various MRI scans. Material and Method… (see more)s: This retrospective study included MRI scans from two open-access and one private dataset, consisting of 3D isotropic 3T TSE T2-weighted (T2w) and 7T MP2RAGE (T1-weighted [T1w] INV1 and INV2, and UNIT1) MRI scans. A deep learning model, RootletSeg, was developed to segment C2-T1 dorsal and ventral spinal rootlets. Training was performed on 76 scans and testing on 17 scans. The Dice score was used to compare the model performance with an existing open-source method. Spinal levels derived from RootletSeg segmentations were compared with vertebral levels defined by intervertebral discs using Bland-Altman analysis. Results: The RootletSeg model developed on 93 MRI scans from 50 healthy adults (mean age, 28.70 years

2025-09-17

ArXiv (preprint)

RootletSeg: Deep learning method for spinal rootlets segmentation across MRI contrasts

Katerina Krejci

Jiri Chmelik

Sandrine B'edard

Falk Eippert

Ulrike Horn

Virginie Callot

Purpose: To develop a deep learning method for the automatic segmentation of spinal nerve rootlets on various MRI scans. Material and Method… (see more)s: This retrospective study included MRI scans from two open-access and one private dataset, consisting of 3D isotropic 3T TSE T2-weighted (T2w) and 7T MP2RAGE (T1-weighted [T1w] INV1 and INV2, and UNIT1) MRI scans. A deep learning model, RootletSeg, was developed to segment C2-T1 dorsal and ventral spinal rootlets. Training was performed on 76 scans and testing on 17 scans. The Dice score was used to compare the model performance with an existing open-source method. Spinal levels derived from RootletSeg segmentations were compared with vertebral levels defined by intervertebral discs using Bland-Altman analysis. Results: The RootletSeg model developed on 93 MRI scans from 50 healthy adults (mean age, 28.70 years

2025-09-17

ArXiv (preprint)

Rootlets-based registration to the PAM50 spinal cord template

Valeria Oliva

Kenneth A. Weber

Abstract Spinal cord functional MRI studies require precise localization of spinal levels for reliable voxel-wise group analyses. Traditiona… (see more)l template-based registration of the spinal cord uses intervertebral discs for alignment. However, substantial anatomical variability across individuals exists between vertebral and spinal levels. This study proposes a novel registration approach that leverages spinal nerve rootlets to improve alignment accuracy and reproducibility across individuals. We developed a registration method leveraging dorsal cervical rootlets segmentation and aligning them non-linearly with the PAM50 spinal cord template. Validation was performed on a multi-subject, multi-site dataset (n = 267, 44 sites) and a multi-subject dataset with various neck positions (n = 10, 3 sessions). We further validated the method on task-based functional MRI (n = 23) to compare group-level activation maps using rootlet-based registration to traditional disc-based methods. Rootlet-based registration showed superior alignment across individuals compared with the traditional disc-based method on n = 226 individuals, and on n = 176 individuals for morphological analyses. Notably, rootlet positions were more stable across neck positions. Group-level analysis of task-based functional MRI using rootlet-based registration increased Z scores and activation cluster size compared with disc-based registration (number of active voxels from 3292 to 7978). Rootlet-based registration enhances both inter- and intra-subject anatomical alignment and yields better spatial normalization for group-level fMRI analyses. Our findings highlight the potential of rootlet-based registration to improve the precision and reliability of spinal cord neuroimaging group analysis.

2025-08-26

Imaging Neuroscience (published)

Monitoring morphometric drift in lifelong learning segmentation of the spinal cord

Enamundram Naga Karthik

Christoph S. Aigner

Elise Bannier

Josef Bednařík

Virginie Callot

Anna Combes

Armin Curt

Gergely Dávid

Falk Eippert

Lynn Farner

Michael G Fehlings

Patrick Freund

Tobias Granberg

Cristina Granziera

RHSCIR Network Imaging Group

Ulrike Horn

Tomáš Horák

Suzanne Humphreys … (see 36 more)

Markus Hupp

Anne Kerbrat

Nawal Kinany

Shannon Kolind

Petr Kudlička

Anna Lebret

Lisa Eunyoung Lee

Caterina Mainero

Allan R. Martin

Megan McGrath

Govind Nair

Kristin P. O’Grady

Jiwon Oh

Russell Ouellette

Nikolai Pfender

Dario Pfyffer

P. Pradat

Alexandre Prat

Emanuele Pravatà

Daniel S. Reich

Ilaria Ricchi

Naama Rotem-Kohavi

Simon Schading-Sassenhausen

Maryam Seif

Andrew C. Smith

Seth Aaron Smith

Grace Sweeney

Roger Tam

Anthony Traboulsee

Constantina A. Treaba

Charidimos Tsagkas

Zachary Vavasour

Dimitri Van De Ville

Kenneth A. Weber

Sarath Chandar

2025-06-12

lifelong-ml.cc/CoLLAs/2025/Workshop_Track (published)

openreview.net

Rootlets-based registration to the spinal cord PAM50 template

Valeria Oliva

Kenneth A. Weber

2025-05-01

arXiv (published)

Normalizing Spinal Cord Compression Measures in Degenerative Cervical Myelopathy.

Maryam Seif

Armin Curt

Simon Schading-Sassenhausen

Nikolai Pfender

P. Freund

Markus Hupp

2025-03-01

The spine journal (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

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 -task seg_sc_ms_lesion_axial_t2w -i .

2025-01-23

medRxiv (preprint)

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

Enamundram Naga Karthik

J. McGinnis

R. Wurm

S. Ruehling

R. Graf

Pierre-Louis Benveniste

M. Lauerer

J. Talbott

R. Bakshi

S. Tauhid

T. Shepherd

A. Berthele

C. Zimmer

B. Hemmer

D. Rueckert

B. Wiestler

J. Kirschke

M. Muehlau

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 -task seg_sc_ms_lesion_axial_t2w -i .

2025-01-23

medRxiv (preprint)

Body size and intracranial volume interact with the structure of the central nervous system: A multi-center in vivo neuroimaging study

René Labounek

Monica T. Bondy

Amy L. Paulson

Mihael Abramovic

Eva Alonso‐Ortiz

Nicole Atcheson

Laura R. Barlow

Robert L. Barry

Markus Barth

Marco Battiston

Christian Büchel

Matthew D. Budde

Virginie Callot

Anna Combes

Benjamin De Leener

Maxime Descoteaux

Paulo Loureiro de Sousa

Marek Dostál

Julien Doyon … (see 74 more)

Adam Dvorak

Falk Eippert

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

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

Maria Marcella Lagana

Cornelia Laule

Christine S. W. Law

Csw Law

Tobias Leutritz

Yaou Liu

Sara Llufriu

Sean Mackey

Allan R. Martin

Eloy Martinez-Heras

Loan Mattera

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 Aaron Smith

Zachary A. Smith

Elisabeth Solana

Yuichi Suzuki

George Tackley

Alexandra Tinnermann

Dimitri Van De Ville

Marios C. Yiannakas

Kenneth A. Weber

Nikolaus Weiskopf

Richard G. Wise

Patrik O. Wyss

Junqian Xu

Christophe Lenglet

Igor Nestrašil

2025-01-01

Imaging Neuroscience (published)