In this study, we defined an operator-independent protocol for reconstructing the anatomical connections originating from fMRI activations in order to demonstrate that results obtained with this protocol are affected by alterations of functional activations. Seven healthy volunteers and two patients who sustained traumatic brain injury underwent an fMRI with a finger tapping task and a DTI scan. Cortical fMRI activations were used directly as seed mask for tractography for the reconstruction of individual motor pathways. On patients we observed a different motor network if compared to healthy subjects. However, when the activations of healthy subjects were used as seed masks for the tractography in patients, we observed for the patients a pattern of connectivity more similar to what was observed for healthy subjects. At the same time, when the activations of patients were used for the tractography on healthy subjects, we obtained patterns of connectivity similar to those obtained for patients. These results show the potential of the integration of fMRI and tractography for clarifying the mechanisms of cortical plasticity in the recovery of motor functions.