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Hi Eugene, Thank you for your advice. I ran the following command: featregapply FEAT.feat/ And it produced a new reg_standard folder as you described. However, the folder only contains the following: example_func.nii.gz mask.nii.gz mean_func.nii.gz reg/ (empty) stats/cope1.nii.gz stats/varcope1.nii.gz I was unable to find a filtered_func file in standard space. Do I need to somehow specify the original filtered_func_data file in the command? I also tried the command: flirt -in filtered_func_data.nii.gz -ref /FEAT.feat/reg/standard.nii.gz -applyxfm -init /FEAT.feat/reg/example_func2standard.mat -out filtered_func_data_MNI152_T1_2mm.nii.gz But this was too computationally expensive and the script was killed. Alternatively, is there a way to do this using the FLIRT GUI? Best, Sam