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Hi FreeSurfer team,
I've been using Infant FreeSurfer for several very young subjects and it works pretty well. But after reviewing the generated surfaces, it looks like pial surface is not extended to fit the cortical grey matter as you can see here: https://secure-web.cisco.com/1bVpNYbCiS9rSsh1DZzM2NKnotXc5MALdQxso7AZkTASVmP... (By the way, did you already observed such surface error for infants using Infant FreeSurfer?)
I was using this command line to generate the volumes of the brain structures: mri_segstats --seg mri/aseg_CCseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab $FREESURFER_HOME/InfantASegStatsLUT.txt --subject $subjectId
So now, I would like to generate the volumes of the brain structres whithout any surface information, to avoid any missleading estimates, is this command line appropriate then? mri_segstats --seg mri/aseg_CCseg.mgz --sum stats/aseg-nosurf.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --euler --ctab $FREESURFER_HOME/InfantASegStatsLUT.txt --subject $subjectId
From what I see, most of the structures volume are identical, except that cerebral grey and white is now provided by the labels and not the surface, and supratentorial/totalgray regions are now missing because only provided by surfaces.
Is there another way to generate statistical values only based on labels? Do you recommend a more classic approach like counting voxels from each structure of interest and then multiplying by pixel resolution? (which is very tedious and error prone in my opinion)
Thanks a lot for your feedback. Florent