Tractography
Preprocessing
Automated global deterministic tractography was performed according to standard protocols. First, diffusion-weighted images were preprocessed using the dtiInit preprocessing pipeline wrapper from Stanford open-source VISTASOFT package version 1.0 (
https://github.com/vistalab/vistasoft) running on MATLAB version 8.6.0 (R2015b) (Math-Works Inc., Natick, MA). The diffusion-weighted images were corrected for eddy currents and head motion, skull-stripped, and tensor fitted.
The following code shows the Matlab function containing the dtinInit command. Prior to running the dtiInit command, it is necessary to merge NifTi images acquired in separate series into one file. The first three lines of the code show this step. There are three arguments for the dtiInit command, 1) the input DTI file in NifTi format; 2) a T1 file--in our case a standard MNI template--to which the DTI images are AC-PC aligned through affine registration and 3) and the DWI parameters (dwParams defined in the line of code above the dtiInit command), the first of which indicates that B vectors were rotated (a necessary step with images from a Siemens scanner, since the dMRI images were rotated for the T1 alignment), and the second indicates that the direction of phase encoding during image acquisition was in the coronal plane, anterior to posterior. A flag value of 1, rather than 2, indicates that phase encoding direction is in the sagittal plane.