High-resolution Diffusion Tensor Imaging of Small Animal Specimens

All specimens were scanned on a 7-Tesla small animal imaging system equipped with an Agilent VnmrJ 4 console. A custom silver solenoid coil (d =13 mm) was used for RF transmission and reception. MR-DTI images were acquired using a 3D diffusion-weighted spin-echo sequence with repetition time (TR)=100 ms, echo time (TE)=14 ms, and b-value=1600 s/mm². The image array size was 400×200×160, over a 20.0×10.0×8.0 mm field of view, producing 50 μm isotropic image resolution. The diffusion sampling protocol included 6 diffusion directions (Jiang and Johnson, 2010 (link)) and 1 non-diffusion-weighted (b0) measurement. Total acquisition time was 7 hours. After registering all individual DWI images (each sensitized to a different diffusion direction) to the b0 image with an affine transform we used the Diffusion Toolkit (Wang et al., 2007 ) to estimate the diffusion tensor and calculate the mean diffusion-weighted image (DWI), axial diffusivity (AD), fractional anisotropy (FA), mean diffusivity (MD), radial diffusivity (RD), and apparent diffusion coefficient (ADC). The DTI parametric images were used as the input for the VBA pipeline.