Hi Ralf,
Is it possible to convert the MRTrix encoding.b to the FSL bvecs/bvals?
Yep: Both mrconvert and mrinfo have the -export_grad_fsl option, which will export to FSL-style bvecs/bvals files with appropriate conversion. Never perform this conversion by manually transposing and splitting / merging the tables.
Can I do the whole process in MRTrix? I mean the registration and then the correct the DW table for the rotation and put it back into the DWI.mif?
The main limitation at the moment is that mrregister only has a mean squared difference image similarity metric, which means that images need to have comparable contrast and intensity scaling in order to drive the registration. Once the registration has been performed, if you use mrtransform to transform your DWIs to the target space, it will detect the diffusion gradient table in the header and perform reorientation automatically.
If I calculate the EigenValues its always only one value with
tensor2metric -vector image? But it should be three. Is there something wrong or are there any options?
Adding -num 1:3 should make tensor2metric provide eigenvalue / eigenvector images with all three components, rather than just the principal vector / value.
Cheers
Rob