If the external program properly uses axis directions information in the image header then you don’t need resampling. If your program ignores axis directions and operates in voxel space then you need resampling.
To resample using an arbitrary region, you can use Crop volume module:
- Input volume: your transformed volume (no need to harden the transform)
- Input ROI: create a new RAS-axes-aligned region of interest by selecting
ROImouse mode on the toolbar, clicking in the middle of the image and a corner in the image, then adjust the size as needed. - Click Apply
ROI place mode on the toolbar:
