Dear Lindsay,
you should study the output of spm_check_orientations to see whether there are some image files that have different orientation and voxel size than the other ones. In that case, it is most likely that you selected a file that does not belong to your dataset. If all images belong to the same dataset, but have different orientations, you (or someone else) did some spatial preprocessing (e.g. realign estimate) on the data before. Artifact repair can not be used on such data. You need to run the toolbox prior to any other preprocessing.
Best regards,
Volkmar
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