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-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.
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