Spatial smoothing before ICA-aroma

fmriprep

#1

Hey all!

I have seen that there is currently no option to spatially smooth data in fMRIPrep, although the ICA-AROMA-paper suggests to apply smoothing (6mm FWHM) before using it (https://doi.org/10.1016/j.neuroimage.2015.02.064). Does somebody know if there is a reason why it is not implemented?
I would like to make use of ICA-AROMA in the pipeline but I don’t know where to employ smoothing. Does anybody have suggestions?

Thank you for your help!


#2

If you run FMRIPREP with --use-aroma option it will internally smooth the data in the same way as described in the original ICA-AROMA paper. Most outputs will stay unsmoothed, however the *bold_space-<space>_variant-smoothAROMAnonaggr_preproc.nii.gz files will be smoothed.

As for specifying custom smoothing kernel there is an issue open: https://github.com/poldracklab/fmriprep/issues/700 - we would love your help implementing it!


#3

Great, thank you a lot!!