Hi Gabe,

Yes, slice-timing correction should be applied AFTER slomoco. Both slomoco and PESTICA perform regressions on the data that require the timing information across slices to be un-altered as much as possible, which rules out slice-timing correction, 3D spatial filtering and spatial normalization.

You can however run 3dvolreg or another volumetric realignment method prior to slomoco/pestica/any other slice-specific nuisance regression method but that would be the most I'd do before these or any other slice-specific nuisance regressions (see Jones TB et al http://www.ncbi.nlm.nih.gov/pubmed/18583...).

Erik