Increased Neurite Orientation-Dispersion and Density in the TgCRND8 Mouse Model of Amyloidosis: Inverse Relation with Functional Connectome Clustering and Modulation by Interleukin-6

Luis M. Colon-Perez; Kristen R. Ibanez; Mallory Suarez; Kristin Torroella; Kelly Acuna; Edward Ofori; Yona Levites; David E. Vaillancourt; Todd E. Golde; Paramita Chakrabarty; Marcelo Febo

The free water elimination procedure was carried out prior to tensor element construction and calculation of FA and mean diffusivity (MD) maps using the DTIFIT program in FSL (Jenkinson et al., 2012) . The free water elimination method uses the Beltrami regularization technique to fit attenuation-normalized diffusion datasets to a bi-exponential model of water diffusion, which estimates the fractional contribution of freely diffusing unrestricted water to the overall signal per voxel (Pasternak et al., 2009) . The free water elimination algorithm is implemented in MATLAB (Natick, MA) using custom code (provided by Dr. Ofer Pasternak, Harvard Medical School) and modified for use with mouse brain diffusion MRI (DeSimone et al., 2017) . The code generates a mouse brain image of free water (indexed from 0 to 1, the latter meaning highest extracellular free water) and a diffusion tensor with free water fraction removed (free water corrected tensor). The corrected tensor was processed using math tools on FSL to produce maps of FA, MD, axial and radial diffusivities (AD and RD, respectively).