User Phil Lewis reasonably modified my first script by using 'imtransform' instead of translation. Still the problem with incorrect transformation of overlapping slices remained. I modified it to calculate the offset by using 'SliceLocation' and not the 'InstanceNumber'. Also there is more returned information in the command window for the user, who can now select input and output directory or overwrite the input files. If there is more than one series in a input folder, this folder will be skipped. Also mixed modalities or modality different than CT, as well as Gantry-free files will not be transformed.
If you have some specific need like transforming several series at the time or similar, feel free to contact me.
The transform matrix had always positiv sign. Now the transform matrix's sign is set to be opposite from the tilt angle.
Wrong sign for negative angles corrected.
Wrong transformation when tilt angle is negative.