I’m looking for some help, I know this topics has been widely covered (sorry) but I didn’t find the solution to my problem.
All the data and the command used to do the plot is available here in case:
Using mrview (which is quite awesome) I can visualize my tensor or main fiber direction after tensor2metric (V1).
I’m doing first really basic processing with 6 directions and dwi2tensor. Everything is perfect.
I can even use the rotation tools and the orientation of the fiber/ellpipsoid si updated in the GUI.
For reproducibility reasons and due to the amount of data I need to process I’m great fan of bash (maybe soon the pipeline functionality of mrtrix).
I’m applying first as simple test a rigid transformation on the data (then I will apply the diffeomorphism).
I cannot find the good command to apply correctly the transformation on the tensor. Using the -reorient_fod yes, the yy, xz, yz images (if the mrtrix convention is [xx,yy,zz,xy,xz,yz]) looks corrupted even a tensor is not really “human readable”) and without the orientation is wrong after extraction of the vector.
(Up) Below is the initial (ground truth ) orientation.
(Middle) Then , after simple mrtransform (wrong)
(Bottom) mrtransform + -reorient_fod yes (corrupted)
ps: in my sample , fiber orientation (V1) is really simple, it should always follow the tangent of the isosurface (radial pattern is clearly wrong in the second image)
Thanks in advance for your help