Hi Adam,
there are 2 steps in your task: apply the transformation and reslice the image with a reference orientation and voxel size. In the batch system, you will find "SPM->Util->Reorient images" to apply the transformation. To reslice the images, use "SPM->Spatial->Realign->Reslice", select your reference image first, followed by the reoriented image(s). Use "Resliced images: 2..n" to only write your reoriented images.
Hope this helps,
Volkmar
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