Hi all,

I want to resample medical volume datasets such that they are always oriented axial. I’ve managed to get it to work more or less using the following code (C# but should be clear enough:)

```
Image lImage = fVolume.InputITKImage;
var lInputSize = lImage.GetSize();
var lMat =lPatientMatrix.Transpose().Inverse().SubMatrix(0, 3, 0, 3);
AffineTransform lTransformReorient = new AffineTransform(3);
lTransformReorient.SetMatrix(new VectorDouble(lMat.ToRowMajorArray()));
var lImageSize = lImage.GetSize();
var lNewSize = new VectorUInt32((lMat * Vector<double>.Build.DenseOfArray(new double[] { lImageSize[0], lImageSize[1], lImageSize[2] }))
.ToArray()
.Select(fDouble => (uint)Math.Abs(fDouble)));
var lSpacing = lImage.GetSpacing();
var lNewSpacing = new VectorDouble((lMat * Vector<double>.Build.DenseOfArray(new double[] { lSpacing[0], lSpacing[1], lSpacing[2] }))
.ToArray()
.Select(fDouble => Math.Abs(fDouble)));
var lOrigin = lImage.GetOrigin();
lOrigin[1] = -lNewSize[1] * lNewSpacing[1]; // test
lResampledImage = SimpleITK.Resample(lImage, lNewSize, lTransformReorient, InterpolatorEnum.sitkLinear, lOrigin, lNewSpacing);
```

The lPatientMatrix contains the orientation of the volume where the column vectors correspond to one direction. E.g. for a coronal view, where the slices go from anterior to posterior, the matrix would be:

1 0 0

0 0 1

0 -1 0

This works more or less.

First question: It seems that ITK uses row vectors as I don’t get a result if I don’t transpose the matrix, is this observation correct?

Second question: When I leave the origin at (0, 0, 0) I see only one slice, that’s why I shift the y component of the origin by the Y Length * Y Spacing. When and how do I shift the origin correctly?

Third question: The volume is resampled correctly, but the Y and Z axis are flipped, ie. positive Y values point to the anterior, and positive Z values point to the feet.

Any advice would be much appreciated!