We performed VBM analysis of the gray matter and white matter volume by using the FMRIB Software Library (FSL) analysis tools (version 5.0.6;
http://www.fmrib.ox.ac.uk/fsl, available in the public domain).
36,37 First, we applied nonlinear noise reduction by using Smallest Univalue Segment Assimilating Nucleus (SUSAN). Second, we segmented the brain from nonbrain tissue, using the Brain Extraction Tool (BET).
38 Subsequently, we performed bias field correction and segmented the brain into gray matter, white matter, and cerebrospinal fluid with the FMRIB Automated Segmentation Tool (FAST) from the Oxford Centre for Functional Magnetic Resonance Imaging of the Brain.
39 We registered all the images to the template of the Montreal Neurological Institute (MNI template) with the FMRIB Linear Image Registration Tool (FLIRT) and the FMRIB Non-linear Image Registration Tool (FNIRT), and applied the registration to the gray and white matter segments.
40,41 The images were modulated to compensate for local expansion. Using the FSL “randomise” analysis tool, we performed nonparametric permutation tests on our data.
42 With VBM, it is possible to measure concentration of gray or white matter (i.e., the proportion of gray or white matter relative to other tissue types within a region) or volume (i.e., the absolute amount of gray or white matter in different regions). In our study, we chose to focus on volume, as neurodegeneration predicts a change in the absolute amount of gray and white matter.