Thank you for getting back to me! I guess my question is if I run fmriprep now using --anat-only and select the output space as T1w, would I need to repeat all of the freesurfer stages of the anatomical pipeline once the pediatric templates are available or can the T1w anatomical outputs be easily transformed into the pediatric template space from T1w space?
Since the freesurfer steps take the longest, I figured I would put the data to run the anatomical steps now, and then just put the functional steps to run once the pediatric templates become available. This would require fmriprep to do an additional transform on the files that get put into the anat subfolder of derivatives (for example, "
anat/sub-<subject_label>_T1w_desc-preproc_T1w.nii.gz" would need to be transformed to "
anat/sub-<subject_label>_[space-<pediatric-template-name>_]desc-preproc_T1w.nii.gz") before the functional pipeline is run so that output functional derivative files (i.e.
func/sub-<subject_label>_[specifiers]_space-<space_label>_desc-preproc_bold.nii.gz) are in the pediatric template space and not T1w/subject native space. I’m was not sure if that would be possible or not.
I’m just curious if running fmriprep with --anat-only now would save me time in the long run. If it is the case that freesurfer would need to be re-run once the new templates become available, it would be better for me to wait. If fmriprep would be able to take the already run freesurfer T1w preproc output and quickly transform it into the new pediatric template space before running the functional pipelines, then I would start running the anatomical pipelines now.
Any thoughts on this or the logistics would be super helpful.