Figure 2. Template construction and optic tract fixel analysis.

a) An unbiased anatomical template was derived from the MPRAGE images of all subjects using the ANTs multivariate template construction algorithm. This template was segmented with Freesurfer tools to construct optic chiasm and LGN masks. b) Another unbiased template was built from the FOD images of the same subjects which were calculated with the constrained spherical deconvolution method. c) The masks defined on the anatomical template were registered to the FOD template coordinates and probabilistic tractography between optic chiasm and LGN was performed. Separately, fixel analysis was performed with this FOD template resulting in the whole brain FC and FD fixel maps for each subject. These fixel maps were then cropped with the optic tract streamlines to obtain fixel values from the optic tract. The whole brain fixel maps on this figure shows an example FC measurement from a subject. The magnitude of the FC value is indicated in a yellow-to-red color scale. The colors on the FOD maps and the tractography streamlines indicate the orientation of the individual FODs and fibers.