Rootlets-based registration to the spinal cord PAM50 template

Spinal cord functional MRI studies require precise localization of spinal levels for reliable voxelwise group analyses. Traditional 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 to the traditional disc-based method. Notably, rootlet positions were more stable across neck positions. Group-level analysis of task-based functional MRI using rootlet-based increased Z scores and activation cluster size compared to 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.

SCIsegV2: A Universal Tool for Segmentation of Intramedullary Lesions in Spinal Cord Injury

Spinal cord injury (SCI) is a devastating incidence leading to permanent paralysis and loss of sensory-motor functions potentially resulting in the formation of lesions within the spinal cord. Imaging biomarkers obtained from magnetic resonance imaging (MRI) scans can predict the functional recovery of individuals with SCI and help choose the optimal treatment strategy. Currently, most studies employ manual quantification of these MRI-derived biomarkers, which is a subjective and tedious task. In this work, we propose (i) a universal tool for the automatic segmentation of intramedullary SCI lesions, dubbed \texttt{SCIsegV2}, and (ii) a method to automatically compute the width of the tissue bridges from the segmented lesion. Tissue bridges represent the spared spinal tissue adjacent to the lesion, which is associated with functional recovery in SCI patients. The tool was trained and validated on a heterogeneous dataset from 7 sites comprising patients from different SCI phases (acute, sub-acute, and chronic) and etiologies (traumatic SCI, ischemic SCI, and degenerative cervical myelopathy). Tissue bridges quantified automatically did not significantly differ from those computed manually, suggesting that the proposed automatic tool can be used to derive relevant MRI biomarkers. \texttt{SCIsegV2} and the automatic tissue bridges computation are open-source and available in Spinal Cord Toolbox (v6.4 and above) via the \texttt{sct\_deepseg -task seg\_sc\_lesion\_t2w\_sci} and \texttt{sct\_analyze\_lesion} functions, respectively.