Dear Meike,
just in case you have not done this yet: before trying to reorient your images you should try to figure out why the images are oriented in the way they are. If you have access to original data from the scanner, it might be better to start with reviewing the process from original (in most cases DICOM) data to NIfTI data. SPM itself or tools like dcm2nii and its successors usually try hard to do a good job in data conversion, keeping as much of scanner-provided orientation information intact as possible.
If you don't have scanner data or neither of the data conversion tools does a good job, the batch module "Batch Editor >> SPM Util >> Reorient Images" is indeed the tool to use. This tool will left-multiply a transformation matrix (in mm space) to the existing transformation matrix of the specified images. The image pixel data will be left unaltered. However, you need to understand which transformation (in world-"mm"-space) you really need. In particular, make sure that L<->R orientation of your reoriented data is correct. You can try the parameters either in "Display" or in the CheckReg context menu (Reorient images). If you found a suitable set of parameters, note them and enter them into your batch or save the resulting transformation matrix and use this in the batch.
Hope this helps
Volkmar
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