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All Publications

  • SCIseg: Automatic Segmentation of T2-weighted Intramedullary Lesions in Spinal Cord Injury. medRxiv : the preprint server for health sciences Karthik, E. N., Valosek, J., Smith, A. C., Pfyffer, D., Schading-Sassenhausen, S., Farner, L., Weber, K. A., Freund, P., Cohen-Adad, J. 2024


    To develop a deep learning tool for the automatic segmentation of T2-weighted intramedullary lesions in spinal cord injury (SCI).This retrospective study included a cohort of SCI patients from three sites enrolled between July 2002 and February 2023. 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 data consisted of T2-weighted MRI acquired using different scanner manufacturers with heterogeneous image resolutions (isotropic/anisotropic), orientations (axial/sagittal), lesion etiologies (traumatic/ischemic/hemorrhagic) and lesions spread across the cervical, thoracic and lumbar spine. The segmentations from the proposed model were visually and quantitatively compared with other open-source baselines. Wilcoxon signed-rank test was used to compare quantitative MRI biomarkers (lesion volume, lesion length, and maximal axial damage ratio) computed from manual lesion masks and those obtained automatically with SCIseg predictions.MRI data from 191 SCI patients (mean age, 48.1 years ± 17.9 [SD]; 142 males) were used for model training and evaluation. SCIseg achieved the best segmentation performance for both the cord and lesions. There was no statistically significant difference between lesion length and maximal axial damage ratio computed from manually annotated lesions and those obtained using SCIseg.Automatic segmentation of intramedullary lesions commonly seen in SCI replaces the tedious manual annotation process and enables the extraction of relevant lesion morphometrics in large cohorts. The proposed model segments lesions across different etiologies, scanner manufacturers, and heterogeneous image resolutions. SCIseg is open-source and accessible through the Spinal Cord Toolbox.

    View details for DOI 10.1101/2024.01.03.24300794

    View details for PubMedID 38699309

    View details for PubMedCentralID PMC11065035

  • Recent developments and future avenues for human corticospinal neuroimaging. Frontiers in human neuroscience Kaptan, M., Pfyffer, D., Konstantopoulos, C. G., Law, C. S., Weber Ii, K. A., Glover, G. H., Mackey, S. 2024; 18: 1339881


    Non-invasive neuroimaging serves as a valuable tool for investigating the mechanisms within the central nervous system (CNS) related to somatosensory and motor processing, emotions, memory, cognition, and other functions. Despite the extensive use of brain imaging, spinal cord imaging has received relatively less attention, regardless of its potential to study peripheral communications with the brain and the descending corticospinal systems. To comprehensively understand the neural mechanisms underlying human sensory and motor functions, particularly in pathological conditions, simultaneous examination of neuronal activity in both the brain and spinal cord becomes imperative. Although technically demanding in terms of data acquisition and analysis, a growing but limited number of studies have successfully utilized specialized acquisition protocols for corticospinal imaging. These studies have effectively assessed sensorimotor, autonomic, and interneuronal signaling within the spinal cord, revealing interactions with cortical processes in the brain. In this mini-review, we aim to examine the expanding body of literature that employs cutting-edge corticospinal imaging to investigate the flow of sensorimotor information between the brain and spinal cord. Additionally, we will provide a concise overview of recent advancements in functional magnetic resonance imaging (fMRI) techniques. Furthermore, we will discuss potential future perspectives aimed at enhancing our comprehension of large-scale neuronal networks in the CNS and their disruptions in clinical disorders. This collective knowledge will aid in refining combined corticospinal fMRI methodologies, leading to the development of clinically relevant biomarkers for conditions affecting sensorimotor processing in the CNS.

    View details for DOI 10.3389/fnhum.2024.1339881

    View details for PubMedID 38332933

    View details for PubMedCentralID PMC10850311

  • Longitudinal motor system changes from acute to chronic spinal cord injury. European journal of neurology Emmenegger, T. M., Pfyffer, D., Curt, A., Schading-Sassenhausen, S., Hupp, M., Ashburner, J., Friston, K., Weiskopf, N., Thompson, A., Freund, P. 2024: e16196


    BACKGROUND AND PURPOSE: In acute spinal cord injury (SCI), magnetic resonance imaging (MRI) reveals tissue bridges and neurodegeneration for 2years. This 5-year study aims to track initial lesion changes, subsequent neurodegeneration, and their impact on recovery.METHODS: This prospective longitudinal study enrolled acute SCI patients and healthy controls who were assessed clinically-and by MRI-regularly from 3days postinjury up to 60months. We employed histologically cross-validated quantitative MRI sequences sensitive to volume, myelin, and iron changes, thereby reflecting indirectly processes of neurodegeneration and neuroinflammation. General linear models tracked lesion and remote changes in volume, myelin- and iron-sensitive magnetic resonance indices over 5years. Associations between lesion, degeneration, and recovery (using the Spinal Cord Independence Measure [SCIM] questionnaire and the International Standards for Neurological Classification of Spinal Cord Injury total motor score) were assessed.RESULTS: Patients' motor scores improved by an average of 12.86 (95% confidence interval [CI] =6.70-19.00) points, and SCIM by 26.08 (95% CI=17.00-35.20) points. Within 3-28days post-SCI, lesion size decreased by more than two-thirds (3days:302.52±185.80mm2 , 28days:76.77±88.62mm2 ), revealing tissue bridges. Cervical cord and corticospinal tract volumes transiently increased in SCI patients by 5% and 3%, respectively, accompanied by cervical myelin decreases and iron increases. Over time, progressive atrophy was observed in both regions, which was linked to early lesion dynamics. Tissue bridges, reduced swelling, and myelin content decreases were predictive of long-term motor score recovery and improved SCIM score.CONCLUSIONS: Studying acute changes and their impact on longer follow-up provides insights into SCI trajectory, highlighting the importance of acute intervention while indicating the potential to influence outcomes in the later stages.

    View details for DOI 10.1111/ene.16196

    View details for PubMedID 38258488

  • Exploring Corticospinal Functional Connectome Using Resting-State Functional Magnetic Resonance Imaging Kaptan, M., Law, C. W., Weber, K., Pfyffer, D., Zhang, X., Maronesy, T., Glover, G., Mackey, S. CHURCHILL LIVINGSTONE. 2023: 17-18
  • Imaging Noxious Thermal Intensity Encoding Along The Neuraxis Using Simultaneous Spinal Cord-Brain Functional Magnetic Resonance Imaging Pfyffer, D., Law, C. W., Weber, K. A., Kaptan, M., Maronesy, T., Glover, G. H., Mackey, S. CHURCHILL LIVINGSTONE. 2023: 76
  • Magnetic resonance spectroscopy investigation in the right human hippocampus following spinal cord injury. Frontiers in neurology Pfyffer, D., Zimmermann, S., Simsek, K., Kreis, R., Freund, P., Seif, M. 2023; 14: 1120227


    Objective: Preclinical studies have shown that cognitive impairments following spinal cord injury (SCI), such as impaired spatial memory, are linked to inflammation, neurodegeneration, and reduced neurogenesis in the right hippocampus. This cross-sectional study aims to characterize metabolic and macrostructural changes in the right hippocampus and their association to cognitive function in traumatic SCI patients.Methods: Within this cross-sectional study, cognitive function was assessed in 28 chronic traumatic SCI patients and 18 age-, sex-, and education-matched healthy controls by a visuospatial and verbal memory test. A magnetic resonance spectroscopy (MRS) and structural MRI protocol was performed in the right hippocampus of both groups to quantify metabolic concentrations and hippocampal volume, respectively. Group comparisons investigated changes between SCI patients and healthy controls and correlation analyses investigated their relationship to memory performance.Results: Memory performance was similar in SCI patients and healthy controls. The quality of the recorded MR spectra was excellent in comparison to the best-practice reports for the hippocampus. Metabolite concentrations and volume of the hippocampus measured based on MRS and MRI were not different between two groups. Memory performance in SCI patients and healthy controls was not correlated with metabolic or structural measures.Conclusion: This study suggests that the hippocampus may not be pathologically affected at a functional, metabolic, and macrostructural level in chronic SCI. This points toward the absence of significant and clinically relevant trauma-induced neurodegeneration in the hippocampus.

    View details for DOI 10.3389/fneur.2023.1120227

    View details for PubMedID 37251221

  • Width of Tissue Bridges Predicts Neurologic Recovery 3 Months After Spinal Cord Injury: a Multi Center Study Pfyffer, D., Smith, A., Weber, K., Draganich, C., Berliner, J., Tefertiller, C., Hothorn, T., Schwab, J., Curt, A., Freund, P. LIPPINCOTT WILLIAMS & WILKINS. 2022