Longitudinal rodent positron emission tomography (PET) studies of stroke and neuromodulation rely on accurate registration to a common atlas space to detect group-level effects. Prior work applying ultra-high frequency low-intensity magnetic stimulation (UHF-LiMS) to a rat model of chronic capsule infarct used affine normalization to a Sprague Dawley MRI template without evaluating that choice. We compare a two-stage (affine and nonlinear) pipeline against an affine- only one for rat PET-to-atlas alignment on the same dataset. Across 32 longitudinal [18F]-FDG PET scans (8 rats, 4 timepoints), the nonlinear stage gave a higher Dice similarity coefficient on every scan, and the gain was significant at the rat level. Jacobian determinants showed no folding on the sampling grid. Group-level linear mixed-effects maps of change from baseline (AFNI 3dLME), computed identically under both pipelines, differ in the size, number and location of their suprathreshold clusters. In this dataset, the registration pipeline is therefore a variable that can change the interpretation of downstream group-level analyses.

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