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
<fis...@nmr.mgh.harvard.edu <mailto:fis...@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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
