Hi MRTrix Experts,
I wanted to get your perspective on warping the subject space diffusion data (preprocessed but not the tensor file) to MNI space. I have calculated the affine and nonlinear components that warp the image to MNI template space and I have rotated the bvecs file according to the rotational-only contribution from the affine matrix to MNI template space using polar decomposition to get the rotational contribution from shearing. I was interested in warping the pre-processed subject space diffusion volumes to MNI space so that we can apply various post-processing tensor fitting methods (i.e. DTI, freewater DTI, DKI etc) using the same pre-processed inputs.
In reading, I see where there are issues warping the tensor file itself in that you must first warp the tensors and then (similar to the ANTS implementation) reorient the tensor based on voxel-wise local deformations.
Do you see this as a major issue when warping the diffusion data as opposed to diffusion tensor prior to fitting using the method I described above?
If it is still an issue does MRTrix or other program you are aware of allow you to enter a voxelwise bvector map per volume instead of bvector file for fitting the tensor?