Dear Professor,
I used fsl to register the DWI images to the T1 images, and it appears that the registration is quite good. However, when I generate the dt.mif using dwi2tensor, it looks fine in the coronal and sagittal views, but there is a clear misalignment in the axial view. I’m not sure where the issue lies. Then, I intended to transform the matrix and apply it to the T1 to register it to the DWI, and then use dwi2tensor to generate the dt.mif, but the situation is similar. I feel that there might be a problem with the registration process. Later, I generated the dt.mif from the original DWI, before registration, and the image was fine. (My data includes b0 and b1000 images.)