I don't know much about the infant stream, but you can try running
mris_preproc. See here
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisV6.0
On 6/7/2022 11:09 AM, Steger Celine wrote:
External Email - Use Caution
Dear FS experts,
We are currently exploring the Infant Freesurfer pipeline for surface
based analysis in our cohort. The generated surfaces seem reasonable,
but now we are wondering, how to proceed. To our understanding, by
looking at the recon-all for adult data, the next step would be to
register each subject to standard space (using the –qcache flag this
happens directly to fsaverage). Since the –qcache flag is not
available in infant_recon_all we would like to clarify if this is not
advised to do so with subjects processed via infant_recon_all or if we
could just proceed with recon_all from here. Is there is any
alternative procedure that should be followed in order to map all
subjects into one space, e.g. creating a cohort specific average?
Kind regards,
Céline
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