All acquired structural images were first corrected for intensity bias by applying a second-order polynomial multiplicative bias field computed via entropy minimization (Likar et al., 2001). The late-echo FSE image was corrected using the bias field computed from the corresponding early-echo image to maintain the ratio of early- and late-echo values at each pixel, which keeps quantities derived from this ratio (e.g., T2) invariant. For each subject and each session, the bias-corrected early-echo FSE image was then registered to the bias-corrected SPGR image using intensity-based nonrigid image registration (Rohlfing and Maurer, 2003) (http://nitrc.org/projects/cmtk). The SPGR, early-echo FSE, and late-echo FSE images were each skull stripped using FSL's Brain Extraction Tool, BET (Smith, 2002). The early- and late-echo brain masks were reformatted into SPGR image space and combined with the SPGR-derived brain mask via label voting (Rohlfing and Maurer, 2005) to form the final SPGR brain mask.
