I am running fMRIPrep on a public dataset and want to perform spatial smoothing using FSL’s SUSAN command. I took a look at the FEAT pre-processing logs, and I see that the last stage of pre-processing is intensity normalisation (grand mean scaling) and temporal filtering. My question is whether fMRIPrep does any grand mean scaling or temporal filtering as I do not want to repeat this if it is already handled by fMRIPrep. I took a look through the fMRIPrep workflows and the html logs and don’t see anything relating to grand mean scaling or temporal filtering, but I may have missed something.
If this is not handled, I’ll add these steps to my pipeline, if it is not, I will stop once smoothing has been performed.
For reference, here are the commands FSL calls after performing smoothing:
- fslmaths prefiltered_func_data_smooth -mul 2.13583203446 prefiltered_func_data_intnorm
- fslmaths prefiltered_func_data_intnorm -Tmean tempMean
- fslmaths prefiltered_func_data_intnorm -bptf 25.0 -1 -add tempMean prefiltered_func_data_tempfilt
- imrm tempMean
- fslmaths prefiltered_func_data_tempfilt filtered_func_data
- fslmaths filtered_func_data -Tmean mean_func
- rm -rf prefiltered_func_data*
Thanks in advance,