Hi,
I am trying to use 3dZcutup to cut slices of a dataset which happens to be saved in ASR orientation. As I supply the range of slices to keep to the command, it tells me that my slice indices pass the number of slices while it does not. Apparently the slice count i this case is in R-L direction. So I suppose 3dZcutup just assumes data is saved such that the last dimension is z dimension.
Can this be fixed?

In addition to this: can you make the program able to cut in any directions? One function that achieves all what 3dYcutup or 3dXcutup would do would be great.

Further related to this: I am using align_anat_epi.py instead of afni_proc.py but I am curious of what is the recommended way to deal with master grid when aligning EPI and anat and when the origin of anatomical and EPI data are off by a lot? Using -master_epi SOURCE in this case might cause cut-off of some of the brain but using BASE could waste a lot of empty space in the grid (typically there are more non-brain stuff in the anatomical image on the bottom). This is why I am trying to cut slices in z-dimension after aligning.

Thanks!
Mingbo