Two Jupyter notebooks are provided.
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01_data_processing notebook
requires acess to private in vivo data (meGRE and T1w) to compute total field maps (using ROMEO[1]), local field and susceptibility maps (requires MATLAB, SEPIA-toolbox[2] and QSM processing toolboxes). It also uses Spinal Cord Toolbox[3] to create spinal cord, gray & white matter masks, and vertebrae level segmentations of the SC
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02_figures_and_metrics
) to reproduce figures and metrics from the paper (FULL CITE):
[1] Dymerska B, Eckstein K, Bachrata B, et al. Phase unwrapping with a rapid opensource minimum spanning tree algorithm (ROMEO). Magn Reson Med. 2021;85(4):2294-2308. [2] Chan KS, Marques JP. SEPIA-Susceptibility mapping pipeline tool for phase images. Neuroimage. 2021;227(117611):117611. [3] De Leener B, Lévy S, Dupont SM, et al. SCT: Spinal Cord Toolbox, an open-source software for processing spinal cord MRI data. Neuroimage. 2017;145(Pt A):24-43. [4]