“…Although manual skull‐stripping is closer to a gold standard for determining ICV, it is time‐consuming and has been largely replaced with automated techniques such as BET (Smith et al., 2002), SPM's integrated tissue segmentation (Ashburner & Friston, 2005), or FreeSurfer watershed algorithm (Dale et al., 2004). As prior authors have noted, the FSL BET can also be a significant source of error (Popescu et al., 2012; Zivadinov et al., 2005) and we found tissue misclassification in several subjects using the default settings; neck cropping and changing the default parameters (−f 0.2 and −B enabled) allowed an optimal solution for our dataset without any significant misclassification errors (Chu et al., 2016). Without any visually prominent errors, several groups have concluded that brain extraction methods are generally a very small source of variance (Clark, Woods, Rottenberg, Toga, & Mazziotta, 2006; Klauschen, Goldman, Barra, Meyer‐Lindenberg, & Lundervold, 2009) and we feel this preprocessing step is unlikely to be a significant source of variance between methods.…”