The issue probably lies with the potential large shift transformation included in the 3dNwarpApply. When 3dNwarpApply deals with grids that are different between the source and master, it zeropads the warp in memory to fit both source and output master grids. If the two datasets start far apart, and the grid resolution is fine, then the memory used can be enormous. Usually there's a good way around this problem by shifting the center of the input dataset as a separate step. Call @Align_Centers to move the center of the errts dataset and other epi datasets with the -child option. That will move the dataset without interpolation by just shifting the origin in the header.