I know I’ve already asked @effigies about this, but after speaking with my lab, I want to approach my question differently. Within fmriprep, I’ve set my output space to MNI152NLin2009cAsym, which means the preproc bold NiFTIs should be spatially similar to the MNI152NLin2009cAsym template, except the voxel dimensions are kept as the original bold NiFTI. So if I was to move to a group analysis, would I only need to resample the images to a 2x2x2 grid? Or should I perform another type of ANTs transform/registration? If only resampling is required, my PI is worried the registrations are not accurate enough, see linked images to overlay:
Additionally, if I wanted to do more processing with the bold NiFTIs in native space (e.g. get an rscore NiFTI map using a seed region) would I use the antsApplyTransforms command with the inverses of the ants_t1_to_mniComposite.h5 and an inverse of the affine.txt (bold_to_t1) to get the bold NiFTIs back into their native space?
To the above point, should there be an option to keep the bold NiFTIs in native space from fmriprep (in addition to the T1w, fsnative, fsaverage*, and template options)? Then we could use our own template (older adult brains have a lot of variability) generated from ANTs, and complete our own registrations when we are ready (e.g. after completing some subject/session level analysis).
One potential argument against: this splits the transform from head motion correction from the transform from the reference image to mni, which goes against the “do everything in one transform” philosophy.
Final thought: how hard would it be to allow users to input their own template image into fmriprep? like specify a path to the template image, or have a directory within BIDs to place templates, like /derivatives/templates/<BIDS_format>_res_XxYxZ_template.nii.gz