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