I used the option you recommended and I noticed that for some subjects the following error came out:
WARNING:: Inconsistent orientations for individual images when attempting to merge.
Merge will use voxel-based orientation which is probably incorrect - *PLEASE CHECK*!
I checked the images i was trying to merge with fslhd and saw that although the orientations are the same the matrix dimensions are different.
Does this mean I cannot merge the two dti images?
Thanks,
maria