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Resting-state functional magnetic resonance imaging (RS-FMRI) has been widely used to map brain functional connectivity, but it is unclear how to probe connectivity within and around lesions. In this study, we characterize RS-FMRI signal time course properties and evaluate different seed placements within and around hemorrhagic traumatic axonal injury (hTAI) lesions. RS-FMRI was performed on a 7 Tesla scanner in a patient who recovered consciousness after traumatic coma and in three healthy controls. Eleven lesions in the patient were characterized in terms of (1) temporal signal-to-noise ratio (tSNR); (2) physiological noise, through comparison of noise regressors derived from the white matter (WM), cerebrospinal fluid (CSF), and gray matter (GM); and (3) seed-based functional connectivity. Temporal SNR at the center of the lesions was 38.3% and 74.1% lower compared with the same region in the contralesional hemisphere of the patient and in the ipsilesional hemispheres of the controls, respectively. Within the lesions, WM noise was more prominent than CSF and GM noise. Lesional seeds did not produce discernable networks, but seeds in the contralesional hemisphere revealed networks whose nodes appeared to be shifted or obscured due to overlapping or nearby lesions. Single-voxel seed analysis demonstrated that placing a seed within a lesion's periphery was necessary to identify networks associated with the lesion region. These findings provide evidence of resting-state network changes in the human brain after recovery from traumatic coma. Furthermore, we show that seed placement within a lesion's periphery or in the contralesional hemisphere may be necessary for network identification in patients with hTAI.

Characterizing Signals Within Lesions and Mapping Brain Network Connectivity After Traumatic Axonal Injury: A 7 Tesla Resting-State FMRI Study