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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 with the traditional disc-based method on n = 226 individuals, and on n = 176 individuals for morphological analyses. Notably, rootlet positions were more stable across neck positions. Group-level analysis of task-based functional MRI using rootlet-based registration increased Z scores and activation cluster size compared with 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.<\/jats:p>","DOI":"10.1162\/imag.a.123","type":"journal-article","created":{"date-parts":[[2025,8,6]],"date-time":"2025-08-06T20:01:51Z","timestamp":1754510511000},"update-policy":"https:\/\/doi.org\/10.1162\/mitpressjournals.corrections.policy","source":"Crossref","is-referenced-by-count":9,"title":["Rootlets-based registration to the PAM50 spinal cord template"],"prefix":"10.1162","volume":"3","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9859-1133","authenticated-orcid":false,"given":"Sandrine","family":"B\u00e9dard","sequence":"first","affiliation":[{"name":"NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, 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Sciences and Mental Health, Italian National Institute of Health, Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0916-9174","authenticated-orcid":false,"given":"Kenneth A.","family":"Weber II","sequence":"additional","affiliation":[{"name":"Neuromuscular Insight Lab, Division of Pain Medicine, Stanford School of Medicine, Palo Alto, CA, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3662-9532","authenticated-orcid":false,"given":"Julien","family":"Cohen-Adad","sequence":"additional","affiliation":[{"name":"NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada"},{"name":"Mila - Quebec AI Institute, Montreal, QC, Canada"},{"name":"Functional Neuroimaging Unit, CRIUGM, Universit\u00e9 de Montr\u00e9al, Montr\u00e9al, QC, Canada"},{"name":"Centre de Recherche du CHU Sainte-Justine, Universit\u00e9 de Montr\u00e9al, 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