Magnetic resonance imaging (MRI) acquisition and analysis

High resolution MRI was undertaken using an 11.7T Bruker Avance instrument (Bruker Biospin, Billerica, MA, USA) running with the Paravision software (version 5.1, Bruker Biospin) to assess brain injury volumes. T2-weighted images (T2WI; repetition time [TR]/echo time [TE]: 2395 ms/10 ms, 20 × 1 mm slices) were acquired and collected on a 256 × 256 matrix with a 2 cm field of view to quantitate edema and extravascular blood.

TBI lesion volumes were evaluated by personnel blinded to the groups. The total lesion volumes (comprising edema and hemorrhage) were determined using the Cheshire image processing software (version 4.3, Parexel, Waltham, MA). Regions of interest (ROIs) were drawn on T2 maps after confirming presence of edema and hemorrhage with T2 relaxation times (>70 msec and 35-45 msec, respectively). Hemorrhage volumes were identified by using the Hierarchical Regional Splitting (HRS) computational method (U.S. patent: 8731261; European patent: 11748009.5-1265, RRID: SCR_016398), based on T2 relaxation times (Ghosh et al., 2011; Ghosh, Sun, Bhanu, Ashwal, & Obenaus, 2014), in which a T2 value of <45 msec was considered hemorrhage. Edema volumes were determined by subtracting hemorrhage volumes from total lesion volumes.

Quantitative T2 maps using all 10 echos were generated using JIM software (RRID: SCR_009589, Xinapse Systems Ltd; West Bergholt, Essex; United Kingdom). The second echo of the T2WI underwent N4 bias field correction (Tustison et al., 2010), which was used for subsequent registration steps. ITK-SNAP’s active contour segmentation (Yushkevich et al., 2006) was used to segment a lesion mask and then subsequently used as an exclusion region in ANTs (Advanced Normalization Tools) deformable b-spline symmetric normalization registration (Tustison & Avants, 2013). The Waxholm MRI atlas (Papp, Leergaard, Calabrese, Johnson, & Bjaalie, 2014) was registered to each individual’s T2WI, and the Waxholm label atlas (separated by hemisphere) was transformed to this resulting image using ANTs (Avants et al., 2011). Native-space T2 values were then extracted using the transformed Waxholm anatomical labels and summarized using GraphPad Prism 7 software (GraphPad Prism, RRID: SCR_002798, San Diego, CA). Some brain regions were excluded from the analysis due to misregistration (see supplemental table 1).