that looks right. You might want to call the output something else so that you don't overwrite the default FS output
On 07/06/2016 01:55 PM, Sabrina Yu wrote: > > 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-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve > <gr...@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 > gr...@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 > <http://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. > > > > _______________________________________________ > 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 gr...@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
