Good question:). It does not look like we are currently creating a stats file for the subfields, which means you will have to do it yourself. You can do it with something like

cd $SUBJECTS_DIR/subject
mri_segstats --seg mri/hippsubfieldseg.mgz --sum stats/hipposub.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject subject  --surf-wm-vol --etiv --ctab $FREESURFERHOME/FreeSurferColorLUT.txt

You can then run asegstats2table specifying hipposub.stats as the stats file

doug




On 8/5/13 3:39 PM, Salil Soman wrote:
Dear Doug and Bruce,

Thank you for your emails. I have also run the -hippo-subfields option on my freesurfer processing. How do I extract those values as tables as well?

Best wishes,

Sal


On Sun, Aug 4, 2013 at 11:10 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
try asegstats2table

cheers
Bruce

On Sun, 4 Aug 2013, Salil Soman wrote:

Hi,
I have a large dataset for which I run freesurfer and confirmed that the
apar+aseg.mgz file is satisfactory. Can someone please recommend the best
way to aggregate all of the volumes/other values generated by freesurfer
into a single table for this dataset? (e.g. subjects as Rows and values by
columns).

Best wishes,

Sla




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--
Salil Soman, MD, MS
Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory
Fellow - Palo Alto War Related Illness and Injury Study Center
WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System