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Spinal Cord Injury Center, Research

Simultaneous brain and spinal cord qMRI to assess focal and remote neurodegeneration after SCI

Project leader: Prof. Dr. Patrick Freund


This project aims to enable the simultaneous analysis of brain and spinal cord MRI data in order to understand the focal and remote neurodegeneration induced by a SCI. 

We use a new template that incorporates the brain and spinal cord in order to perform voxel-wise statistical analysis within the SPM framework (Blaiotta et al 2018, Neuroimage).

The clinical validity of the pipeline has been demonstrated (Azzarito et al 2020, HBM). This approach revealed trauma-induced changes across the sensorimotor system in the cord and brain in SCI patients, comparable to conventional analysis methods. This unique method will also be used to assess the dynamic neurodegenerative processes in the spinal cord and brain post-SCI (Freund et al 2019, Lancet Neurology).

Preliminary results indicate that over 5 years atrophy endures both at the level of the spinal cord and brain. It is also envisioned to apply this tool to patients suffering from multiple sclerosis in collaboration with UCSF.



Simultaneous brain and spinal cord qMRI to assess focal and remote neurodegeneration after SCI



Azzarito, Michela, Sreenath P. Kyathanahally, Yaël Balbastre, Maryam Seif, Claudia Blaiotta, Martina F. Callaghan, John Ashburner, and Patrick Freund. 2020. “Simultaneous Voxel-Wise Analysis of Brain and Spinal Cord Morphometry and Microstructure within the SPM Framework.” Human Brain Mapping, no. August 2020: 220–32.

Blaiotta, Claudia, Patrick Freund, M. Jorge Cardoso, and John Ashburner. 2018. “Generative Diffeomorphic Modelling of Large MRI Data Sets for Probabilistic Template Construction.” NeuroImage 166 (October 2017): 117–34.

Freund, Patrick, Maryam Seif, Nikolaus Weiskopf, Karl Friston, Michael G. Fehlings, Alan J. Thompson, and Armin Curt. 2019. “MRI in Traumatic Spinal Cord Injury: From Clinical Assessment to Neuroimaging Biomarkers.” The Lancet Neurology 18 (12): 1123–35.