Hi,

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:

https://filesender.renater.fr/?s=download&token=edd7f071-d9bf-4370-a533-a49659373999

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

Valéry