Dynamic reorganization of functional connectome gradients reveals time-specific recovery patterns after stroke

Stroke, a leading cause of death and disability worldwide, severely disrupts brain functional organization and cognitive abilities. Previous research has mainly focused on discrete functional network changes post-stroke, but how stroke affects whole-brain functional hierarchy and its relationship to cognitive recovery remains poorly understood. In this exploratory longitudinal study, we used connectome gradient mapping in 33 patients with first-ever stroke and 21 healthy controls to examine how stroke affects large-scale functional network organization across an early post-stroke(∼2 weeks), a subacute stage (3 months), and a chronic stage (1 year). By projecting functional connectivity patterns onto a low-dimensional gradient space, we found that although overall gradient structure remained relatively stable at the group level, individual patients exhibited significant deviations (EDfunc) from the healthy topology, most prominently at the early post-stroke across visual, somatomotor, ventral attention, and control networks. Furthermore, EDfunc showed time-specific associations with cognitive functions: broad negative correlations with visuospatial attention in the early post-stroke, transitioning to more selective associations with motor and attention measures in the chronic stage. In addition, dynamic interhemispheric functional imbalances emerged in the subacute and chronic stages. Taken together, these findings provide preliminary, hypothesis-generating evidence for dynamic reorganization of whole-brain functional hierarchy following stroke, and suggest that connectome gradient analysis and EDfunc may offer a sensitive framework for monitoring recovery and informing individualized rehabilitation strategies, pending confirmation in larger multi-center cohorts.