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I'm doing a simple FEAT pre-processing of a timeseries which does MCFLIRT and filtering. It writes out the following files: .feat/example_func.nii.gz .feat/filtered_func_data.nii.gz .feat/mask.nii.gz .feat/mean_func.nii.gz .feat/reg/example_func2standard.nii.gz .feat/reg/example_func.nii.gz .feat/reg/standard.nii.gz I've used the following command on other analyses to nonlinearly register the timeseries to the MNI template: applywarp -i filtered_func_data.nii.gz -r MNI_T1_2mm.nii.gz -o MNItimeseries.nii.gz -r example_func2standard_warp.nii.gz But the example_func2standard_warp.nii.gz file is not being written out for preprocessing only. How would I register the preprocessed timeseries to the MNI template?