good questions indeed about our data...
i was confused at first about 46 being number of slices, because I was doing all the acquisitions and I know that slice thickness in out epi scans is .5 cm and the total number of slices was less than ~35, BUT then i realized that we did all the pre-processing in SPM and normalized it to 3x3x3 mm voxel size and this way thare are 46 slices.
so what numbers should I used for to3d to work properly and do the error checking?
as for the second question, entire volume was not acquired at the same time but SPM normalization kind of messes it up anyway... in case I do wanna let to3d know about, alt+z or something like it would be the way to do it?