The aim of this work was to develop an automated pipeline to study structural changes in a rat model of TBI using T1/T2-weighted images. Our results show that the CCI model causes focal alterations in grey matter in the proximity of the injury, with a visible edema 14 days after injury in T2-weighted images, plus damage in the white matter (corpus callosum). These hyper-intense lesions complicate registration and require optimisation of the affine step, together with skull stripping of the brain of injured rats.
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