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Dear fMRIBbers, I'd appreciate your suggestions for the following issues: I have 13 3.5mm oblique functional slices (parallel to the lateral sulcus) that I want to register on a whole head anatomical scan. The information available appears to be a bit limited for straight-forward registration with 6 dof, and therefore I have first rotated the anatomical scans around the y axis over the appropriate angle (known from the experiment), so that the orientation of the new anatomical scan corresponds to that of the functional scans. Then I want to do the registration with only tranlational dofs. Here I get some problems: 1) running flirt from the command line with -dof 3 gives an error message (erroneous dof 3, using 6 instead), and the result is a quite incorrectly rotated scan. Adding -nosearch does not change this (though it should according to the explanation of this option), nor does adding -searchrx -1 1 etc to limit the rotation angle to 1 degree: the result remains a rotation about 30, 40, 50 or so degrees. Running flirt from the FEAT GUI with dof 3 makes that dof 6 is actually applied but a translation schedule is invoked as well, which leads to a pure translational registration, however with a mismatch in the result of sometimes 2-3 cm especially in the inferior/superior direction. My question is: how can I achieve an only translational registration which will also produce a good match? Other options? Other cost function? etc 2)Once this is solved, probably by some command line run of flirt, what should I do next to make sure that the proper results are stored in the various feat subdirectories so that a) the result of the individual report.html is correctly updated for the registration and b) the proper files etc are substituted to allow for a higher level analysis which uses the feat (sub)directories as input? This I cannot exactly recover from the report.com/log files. Thanks in advance for your help, regards, Ruurd Schoonhoven VUmc Amsterdam