Thank you for those details. It looks like AROMA is producing outputs in space: MNI152NLin6Asym upsampled to 2mm resolution (see discussion here) while the command --output-spaces MNI152NLin6Asym produces outputs in native resolution (which looks like it is 3x3x3.3mm in your case).
Again, I see two choices:
1/ either you re-run again fmriprep ( if you re-use the working directory (option -w) not everything will be re-run again) with --output-spaces MNI152NLin6Asym:res-2 (more details on this option here)
2/ you can resample the bold mask in the 2mm resolution. Several possibilities:
- using FSLeyes: load the two images, the mask and the smoothed aroma image, then highlight the mask image and click on:
Tools > Resample imageand on the top right select the smoothed aroma image, choosing “nearest neighbor” for interpolation: voilà! - with flirt:
flirt -in brain mask_space-MNI152NLin6Asym_in_native resolution -ref smoothed_aroma_space-MNI152NLin6Asym_in_2mm_resolution -out brain mask_space-MNI152NLin6Asym_in_2mm resolution -interp nearestneighbour -applyxfm