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 … (see 11 more)

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… (see more) 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 (published)

Automatic Segmentation of the Spinal Cord Nerve Rootlets

Jan Valošek

Theo Mathieu

Raphaëlle Schlienger

Olivia S. Kowalczyk

Precise identification of spinal nerve rootlets is relevant to delineate spinal levels for the study of functional activity in the spinal co… (see more)rd. The goal of this study was to develop an automatic method for the semantic segmentation of spinal nerve rootlets from T2-weighted magnetic resonance imaging (MRI) scans. Images from two open-access MRI datasets were used to train a 3D multi-class convolutional neural network using an active learning approach to segment C2-C8 dorsal nerve rootlets. Each output class corresponds to a spinal level. The method was tested on 3T T2-weighted images from datasets unseen during training to assess inter-site, inter-session, and inter-resolution variability. The test Dice score was 0.67 +- 0.16 (mean +- standard deviation across rootlets levels), suggesting a good performance. The method also demonstrated low inter-vendor and inter-site variability (coefficient of variation= 1.41 %), as well as low inter-session variability (coefficient of variation= 1.30 %) indicating stable predictions across different MRI

2024-07-02

Imaging Neuroscience (published)

Open Source in Lab Management

This document explores the advantages of integrating open source software and practices in managing a scientific lab, emphasizing reproducib… (see more)ility and the avoidance of pitfalls. It details practical applications from website management using GitHub Pages to organizing datasets in compliance with BIDS standards, highlights the importance of continuous testing for data integrity, IT management through Ansible for efficient system configuration, open source software development. The broader goal is to promote transparent, reproducible science by adopting open source tools. This approach not only saves time but exposes students to best practices, enhancing the transparency and reproducibility of scientific research.

2024-05-13

ArXiv (preprint)

Open Source in Lab Management

This document explores the advantages of integrating open source software and practices in managing a scientific lab, emphasizing reproducib… (see more)ility and the avoidance of pitfalls. It details practical applications from website management using GitHub Pages to organizing datasets in compliance with BIDS standards, highlights the importance of continuous testing for data integrity, IT management through Ansible for efficient system configuration, open source software development. The broader goal is to promote transparent, reproducible science by adopting open source tools. This approach not only saves time but exposes students to best practices, enhancing the transparency and reproducibility of scientific research.

2024-05-13

ArXiv (preprint)

Open Source in Lab Management

This document explores the advantages of integrating open source software and practices in managing a scientific lab, emphasizing reproducib… (see more)ility and the avoidance of pitfalls. It details practical applications from website management using GitHub Pages to organizing datasets in compliance with BIDS standards, highlights the importance of continuous testing for data integrity, IT management through Ansible for efficient system configuration, open source software development. The broader goal is to promote transparent, reproducible science by adopting open source tools. This approach not only saves time but exposes students to best practices, enhancing the transparency and reproducibility of scientific research.

2024-05-13

ArXiv (preprint)

Calibration-free parallel transmission of the cervical, thoracic, and lumbar spinal cord at 7T.

Christoph S. Aigner

Manuel F. Sánchez Alarcon

Alexandre D'Astous

Eva Alonso‐Ortiz

Sebastian Schmitter

PURPOSE To address the limitations of spinal cord imaging at ultra-high field (UHF) due to time-consuming parallel transmit (pTx) adjustment… (see more)s. This study introduces calibration-free offline computed universal shim modes that can be applied seamlessly for different pTx RF coils and spinal cord target regions, substantially enhancing spinal cord imaging efficiency at UHF. METHODS A library of channel-wise relative B 1 +

2024-05-10

Magnetic Resonance in Medicine (published)

Calibration-free parallel transmission of the cervical, thoracic, and lumbar spinal cord at 7T.

Christoph S. Aigner

Manuel F. Sánchez Alarcon

Alexandre D'Astous

Eva Alonso‐Ortiz

Sebastian Schmitter

PURPOSE To address the limitations of spinal cord imaging at ultra-high field (UHF) due to time-consuming parallel transmit (pTx) adjustment… (see more)s. This study introduces calibration-free offline computed universal shim modes that can be applied seamlessly for different pTx RF coils and spinal cord target regions, substantially enhancing spinal cord imaging efficiency at UHF. METHODS A library of channel-wise relative B 1 +

2024-05-10

Magnetic Resonance in Medicine (published)

Calibration‐free parallel transmission of the cervical, thoracic, and lumbar spinal cord at <scp>7T</scp>

Christoph S. Aigner

Manuel F. Sánchez Alarcon

Alexandre D'Astous

Eva Alonso‐Ortiz

Sebastian Schmitter

2024-05-10

Magnetic Resonance in Medicine (published)

Repeat it without me: Crowdsourcing the T1 mapping common ground via the ISMRM reproducibility challenge.

Mathieu Boudreau

Agah Karakuzu

Ecem Bozkurt

Madeline Carr

Marco Castellaro

Luis Concha

Mariya Doneva

Seraina A. Dual

Alex Ensworth

Alexandru Foias

Véronique Fortier

Refaat E. Gabr

Guillaume Gilbert

Carri K. Glide‐Hurst

Matthew Grech‐Sollars

Siyuan Hu

Oscar Jalnefjord

Jorge Jovicich

Kübra Keskin … (see 22 more)

Peter Koken

Anastasia Kolokotronis

Simran Kukran

Nam G. Lee

Ives R. Levesque

Bochao Li

Dan Ma

Burkhard Mädler

Nyasha G. Maforo

Jamie Near

Erick Pasaye

Alonso Ramirez‐Manzanares

Ben Statton

Christian Stehning

Stefano Tambalo

Ye Tian

Chenyang Wang

Kilian Weiss

Niloufar Zakariaei

Shuo Zhang

Ziwei Zhao

Nikola Stikov

PURPOSE T1 mapping is a widely used quantitative MRI technique, but its tissue-specific values remain inconsistent across protocols, sites, … (see more)and vendors. The ISMRM Reproducible Research and Quantitative MR study groups jointly launched a challenge to assess the reproducibility of a well-established inversion-recovery T1 mapping technique, using acquisition details from a seminal T1 mapping paper on a standardized phantom and in human brains. METHODS The challenge used the acquisition protocol from Barral et al. (2010). Researchers collected T1 mapping data on the ISMRM/NIST phantom and/or in human brains. Data submission, pipeline development, and analysis were conducted using open-source platforms. Intersubmission and intrasubmission comparisons were performed. RESULTS Eighteen submissions (39 phantom and 56 human datasets) on scanners by three MRI vendors were collected at 3 T (except one, at 0.35 T). The mean coefficient of variation was 6.1% for intersubmission phantom measurements, and 2.9% for intrasubmission measurements. For humans, the intersubmission/intrasubmission coefficient of variation was 5.9/3.2% in the genu and 16/6.9% in the cortex. An interactive dashboard for data visualization was also developed: https://rrsg2020.dashboards.neurolibre.org. CONCLUSION The T1 intersubmission variability was twice as high as the intrasubmission variability in both phantoms and human brains, indicating that the acquisition details in the original paper were insufficient to reproduce a quantitative MRI protocol. This study reports the inherent uncertainty in T1 measures across independent research groups, bringing us one step closer to a practical clinical baseline of T1 variations in vivo.

2024-05-10

Magnetic Resonance in Medicine (published)

Repeat it without me: Crowdsourcing the T1 mapping common ground via the ISMRM reproducibility challenge

Mathieu Boudreau

Agah Karakuzu

Ecem Bozkurt

Madeline Carr

Marco Castellaro

Luis Concha

Mariya Doneva

Seraina A. Dual

Alex Ensworth

Alexandru Foias

Véronique Fortier

Refaat E. Gabr

Guillaume Gilbert

Carri K. Glide‐Hurst

Matthew Grech‐Sollars

Siyuan Hu

Oscar Jalnefjord

Jorge Jovicich

Kübra Keskin … (see 22 more)

Peter Koken

Anastasia Kolokotronis

Simran Kukran

Nam G. Lee

Ives R. Levesque

Bochao Li

Dan Ma

Burkhard Mädler

Nyasha G. Maforo

Jamie Near

Erick Pasaye

Alonso Ramirez‐Manzanares

Ben Statton

Christian Stehning

Stefano Tambalo

Ye Tian

Chenyang Wang

Kilian Weiss

Niloufar Zakariaei

Shuo Zhang

Ziwei Zhao

Nikola Stikov

T1 mapping is a widely used quantitative MRI technique, but its tissue‐specific values remain inconsistent across protocols, sites, and ve… (see more)ndors. The ISMRM Reproducible Research and Quantitative MR study groups jointly launched a challenge to assess the reproducibility of a well‐established inversion‐recovery T1 mapping technique, using acquisition details from a seminal T1 mapping paper on a standardized phantom and in human brains.

2024-05-10

Magnetic Resonance in Medicine (published)

Quantifying neurodegeneration of the cervical cord and brain in degenerative cervical myelopathy: A multicentre study using quantitative <scp>magnetic resonance imaging</scp>

Patrick Freund

Viveka Boller

Tim M. Emmenegger

Muhammad Akbar

Markus Hupp

Nikolai Pfender

Claudia A. M. Gandini Wheeler-Kingshott

Michael G. Fehlings

Armin Curt

Maryam Seif

2024-05-07

European Journal of Neurology (published)

Quantifying neurodegeneration of the cervical cord and brain in degenerative cervical myelopathy: A multicentre study using quantitative magnetic resonance imaging

Patrick Freund

Viveka Boller

Tim M. Emmenegger

Muhammad Akbar

Markus Hupp

Nikolai Pfender

Claudia A. M. Gandini Wheeler-Kingshott

Michael G. Fehlings

Armin Curt

Maryam Seif

Simultaneous assessment of neurodegeneration in both the cervical cord and brain across multiple centres can enhance the effectiveness of cl… (see more)inical trials. Thus, this study aims to simultaneously assess microstructural changes in the cervical cord and brain above the stenosis in degenerative cervical myelopathy (DCM) using quantitative magnetic resonance imaging (MRI) in a multicentre study.

2024-05-07

European Journal of Neurology (published)