vborient

From VoxBoWiki

vborient is a command-line tool that makes it easy to change a 3D or 4D image file's orientation. By using the -from flag, you can have VoxBo ignore the orientation found in the header of the input file, and use the specified orientation instead. For reasons of convenience, vborient also includes a function to de-interleave your volume.

vborient uses the three-letter VoxBo orientation codes.

For example, if you want to change an interleaved ASL cube called asl.cub to an RPI cube called rpi.cub, type:

vborient asl.cub rpi.cub RPI -from ASL

Here's the help text:

VoxBo vborient (v1.8.5pre8/May  6 2010)
summary:
  change orientation of a 3D or 4D volume
usage:
  vborient  <infile> <outfile> <new orientation> [flag]
flags:
  -from <orient>   specify orientation of input volume
  -i               data should be interleaved
notes:
  Orientation codes are three-letter codes, with the letters
  specifying orientation of the x, y, and z axes, respectively.  The
  letter codes are: (R)ight, (L)eft, (I)nferior, (S)uperior,
  (A)nterior, and (P)osterior.  So an axial image in radiological
  orientation is RPI.

  If the -from flag is not present, the orientation must be indicated
    in the file.

  If the -i flag is specified, the volume will be de-interleaved.