NAME

       PermuteFlipImageOrientationAxes - part of ANTS registration suite

DESCRIPTION

       Usage:  PermuteFlipImageOrientationAxes  ImageDimension   inputImageFile   outputImageFile
       xperm yperm {zperm}  xflip yflip {zflip}  {FlipAboutOrigin}

       for 3D:
              PermuteFlipImageOrientationAxes 3  in.nii out.nii   2 0 1  1 1 1

              would map z=>x, x=>y, y=>z and flip each for 2D:  PermuteFlipImageOrientationAxes 2
              in.nii out.nii   1 0  1 0 would map x=>y, y=>x and flip x

              0  1 2 for permute factors gives no axis permutation 1 2 0 maps y to x,  z to y and
              x to z the flip values are boolean -  0 1 0 would flip the y-axis only

              The FlipAboutOrigin boolean lets you flip about the coordinate set in the origin