Hello,
I have a couple of questions about the wmparc.stats file generated. What volume is the data based on? Has the intensity of the volume been corrected? 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?
Thank you in advance.
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
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.htmlhttp://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.
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.
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 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
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Sabrina Yu