“…Investigators have applied a myriad of published proprietary and open‐source methods to quantify brain volume loss (Giorgio, Battaglini, Smith, & De Stefano, 2008), leading to heterogeneous segmentation procedures across sites and studies, without any agreed‐upon standard approach (Bermel & Bakshi, 2006). This heterogeneity is brought to the surface by the regular incorporation of whole‐brain atrophy as a supportive outcome measure in Phase III MS therapeutic clinical trials, in which registration‐based {affine‐fit to an external multiple subject brain size atlas, e.g., normalized brain parenchymal volume [BPV; OPERA I/II (Hauser et al., 2017), FREEDOMS (De Stefano et al., 2016), ALLEGRO (Comi et al., 2012), DEFINE (Arnold et al., 2014)]}, or proportional‐based {scaled to the subject's own intracranial cavity, e.g., brain parenchymal fraction [BPF; CARE‐MS I/II (Arnold et al., 2016), AFFIRM (Miller et al., 2007), TEMSO (O'Connor et al., 2011)]} methods have been employed. Moreover, this challenge is amplified by the observations that the analysis of the same MRI image sets using different segmentation pipelines can produce conflicting findings (O'Connor et al., 2011; Radue et al., 2017; Rovaris, Comi, Rocca, Wolinsky, & Filippi, 2001; Sormani et al., 2004), which hamper the ability to draw firm conclusions on therapeutic effects, and may invalidate the comparison of results across trials.…”