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DICOM Raw data folder => DICOM rawimages => nifti rawimages => same file to T1preprocess subject series folders => average of series to T1_initinative => same fiel file to T1_manual2MNI => resliced in T1_ref_vox..bb...
During preprocessing, CSPM checks to see whether the T1_manual2MNI file has shifted; if so, it re-runs subsequent steps, starting from the reslicing. The advantage of this approach is that we retain the original native space T1's, and at least in SPM12 we can save the re-orientation parameters for later use, in case we re-convert the nift nifti files, or want to apply the reorientation to other images.