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The effect of T1 signal on FSL voxel-based morphometry modulated GM density and FreeSurfer cortical thickness is explored. The techniques rely on different analyses, but both are commonly used to detect spatial changes in GM. Standard pipelines show FSL voxel-based morphometry is sensitive to T1 signal alterations within a physiologic range, and results can appear discordant between FSL voxel-based morphometry and FreeSurfer cortical thickness. Care should be taken in extrapolating results to the effect on brain volume.

Influence of T1-Weighted Signal Intensity on FSL Voxel-Based Morphometry and FreeSurfer Cortical Thickness