Hi, 


Thanks for the quick reply. I just want to confirm that my command is correct for changing the input volume to orig.mgz: 


mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/orig.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/orig.mgz --in-intensity-name orig --in-intensity-units MR --subject SUBJECT --surf-wm-vol --ctab /Applications/freesurfer/WMParcStatsLUT.txt --etiv 


Thanks

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N Greve <greve@nmr.mgh.harvard.edu>
Sent: Wednesday, July 6, 2016 10:21:41 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Intensity stats question
 


On 07/06/2016 01:05 PM, Sabrina Yu wrote:
>
> Hello,
>
>
> I have a couple of questions about the wmparc.stats file generated.
> What volume is the data based on?
>
norm.mgz
>
> Has the intensity of the volume been corrected?
>
Yes
>
> I just need the average voxel intensity over the ROIs, but am unsure
> if this intensity is based on an intensity normalized brain volume.
>
>
> Is it possible to change the input volume for wmparc.stats to orig.mgz?
>
Look in the subject/scripts/recon-all.log file for the mri_segstats
command that generates the wmparc.stats file
>
>
> Thank you in advance.
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

_______________________________________________
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.