Oct 14, 2026J/K move · Enter open · S save
Elmira Mirzabeigi, Zahra Khalilzad, Taylor Snowden-Richardson, Jesus Eduardo Lugo Arce+3
Faubert Laboratory, School of Optometry, Université de Montréal, 3744 Jean-Brillant, Montréal, Québec H3T 1P1, Canada · Department of Psychology, University of Victoria, 3800 Finnerty Road, Victoria, British Columbia V8P 5C2, Canada · Division of Medical Sciences, University of Victoria, 3800 Finnerty Road, Victoria, British Columbia V8P 5C2, Canada
Reliable brain-mask transfer into native fluid-attenuated inversion recovery (FLAIR) space can fail when T1-to-FLAIR rigid registration is unstable. We developed A
3PreCore, a six-degree-of-freedom rigid-registration strategy that aligns the full bias-corrected T1-weighted image to native FLAIR using normalized mutual information while preserving the established T1-space anatomical mask. We also introduced extended quantitative quality control (E-QC), which characterizes mask extent, field-of-view-relative position, FLAIR intensity support, boundary support, inferior morphology, and pairwise geometric disagreement. In 78 participants with paired T1-weighted and FLAIR imaging, A
3PreCore was compared with fsl_anat and the Brain Extraction Tool (BET). Gross rigid-body misregistration occurred in 21/78 fsl_anat outputs (26.9%) and 0/78 A
3PreCore outputs (exact two-sided McNemar p=9.54 x 10^-7). Among 57 participants without gross fsl_anat misregistration, A
3PreCore preserved close agreement (median Dice=0.993; median paired Delta NMI=-0.00007, p=0.429). A
3PreCore remained broadly concordant with BET (median Dice=0.955), with less inferior and extracranial extension in representative comparisons. Method-blinded neuroscientists ranked A
3PreCore first in 35/40 participants (87.5%). E-QC additionally exposed severe orientation-related disagreement not evident from global descriptors or centroid displacement alone. These findings support A
3PreCore as a robust native-FLAIR brain-mask transfer strategy and E-QC as a complementary framework for multidimensional mask characterization and participant-specific geometric quality control.