Dear Elveda,
I can only guess that your batch/script tries to run e.g. Coregister but fails to set the filename of the reference image. You should check the order and format of your batch inputs in your script. File names must be entered as cell strings like this {'/path/to/my/file.img'}. For the reference image, the name must be a valid image filename ending with .nii or .img (with or without a ,X frame number).
Hope this helps,
Volkmar
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