Dear Suzanne,
are you using 4D-NIFTI files? In that case, SPM will most likely create empty images for excluded frames. As long as you remember to select only the relevant frames in later stages of processing, that should be fine (you will be wasting some space on your harddisk, though). This should also work with batch dependencies. This is because the frame number is not recalculated when writing to the output file, i.e. frame fMRI_xyz.nii,7 will become frame rfMRI_xyz.nii,7 even if it is the first frame to be written out.
If you don't like the empty frames, you might either want to work with 3D files or exclude the unwanted frames from your 4D file before doing any other processing. As a side effect, if your data is stored on a network filesystem, access to data might be much faster for 3D than 4D files.
Best,
Volkmar
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