If the problem you describe here pertains to the same dataset as the one under Asymmetric Helical refinement (sym or convergence problem), where the resolution is apparently not Nyquist-limited, you may consider down-sampling the movies. Movie down-sampling is not currently implemented in CryoSPARC and would therefore have to be performed with an external program.
Again assuming that cufftAllocFailed occurred during processing of the dataset described in your other topic, you may be able to treat the filament asymmetric unit as a single particle, and reduce the extraction box size accordingly, aiming to extract (and pad) the asymmetric unit, but not necessarily entire filaments.
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