I appreciate it if you help me with a question on your longitudinal processing pipeline. If I use FreeSurfer to generate an unbiased T1 image template from N time points (non-linear registration), then how can I apply the within subject transformation matrix (Jacobian matrix) to that subject's DTI maps. 

Does FreeSurfer save the transformation matrix from N.Time-Points toward Template image? and if so, in which folder directory it will be saved? 

Also, given that FS uses vertices, should I first convert that transformation matrix to voxel space  (eg. using surf2voxels ?) and then multiply that into different time-points of one's DTI images.

Hope my questions are clear and looking forward to hearing from you:-)

Best 

Suzan