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 mailto: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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.-- 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