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Hi FreeSurfer experts,

I have a few questions regarding the infant freesurfer tool, which I'm currently trying to get up and running on my neonatal data.

Question 1: I've run the command infant_recon_all --s SUBJ --age 0, but I was wondering if there are specific additional flags that you would recommend. The main thing we're wanting to look at right now is total cortical gray and cerebral white matter volumes (L and R hemispheres separate). Should I be including --gmwm2 and --force (or any others)?

Questions 2,3: After running that command (without the extra flags) I couldn't find any aseg.stats. I was wondering if there's something I've either done wrong, or should be including. Also, which of brainvol.stats, lh.aparc.stats and rh.aparc.stats should I use for the most accurate measure of cortical gray volume and cerebral white volume?

Question 4: I saw on this mailing list a thread about quality-checking/ manual editing of the outputs, and that this is currently not available for the infant tool. Is that still the case, i.e. we can check the outputs visually but not make corrections. If so, would we then just run the infant_recon_all command and use those outputs as is?

Sorry for the load of questions. I've attached the infant_recon_all log file in case that's needed.

Thanks very much, --

Fleur Warton

Postdoctoral Research Fellow Division of Biomedical Engineering Faculty of Health Sciences University of Cape Town