Hi Peng Ren,
Use 3dresample to alter the orientation when the current orientation is accurate, but not what you want (i.e. the views look correct when shown by the afni GUI). If the orientation is NOT correct (i.e. the views do not look correct in the afni GUI), then use 3drefit to adjust them.
The former leaves the brain in the same location in space, but changes it on disk. The latter alters the location of the data in space, e.g. because it has the anterior brain pointing left, not anterior, one would want to change the definition of where anterior is.
Which position are you in? When viewing the brains in the GUI, do they look correct or not?
- rick
