Thanks Mark! 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 2013/4/17 Mark Jenkinson <[log in to unmask]> > Hi, > > Just use -t to merge 4D diffusion datasets. > > All the best, > Mark > > > maria estanqueiro <[log in to unmask]> wrote: > >