Thanks Doug, those are calculated by pctsurfcon correct? Is there also a way to separately measure white matter intensity, not a gray-white contrast?
Thanks On Fri, Dec 4, 2015 at 10:38 AM -0800, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>> wrote: there should be a {lh,rh}.w-g.pct.stats files in $SUBJECTS_DIR/subject/stats. That will have the mean gray-white contrast for each ROI in the aparc. Does that work for you? On 12/04/2015 01:29 PM, Sabrina Yu wrote: > I think averaged over an ROI is what is best. Any way to do this in > FreeSurfer? > > Thanks, > Sabrina > > > > On Fri, Dec 4, 2015 at 10:16 AM -0800, "Douglas N Greve" > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > on a voxel-by-voxel basis or averaged over an ROI? > > On 12/04/2015 12:56 PM, Sabrina Yu wrote: > > Absolutely, sorry for the confusion. I am looking at decreased > > ipsilesional myelination signal intensity in patients with unilateral > > strokes. The goal is to run the T1 scans through FreeSurfer, then > > determine the ratio of signal intensity - contralesional: ipsilesional. > > > > Thanks, > > Sabrina > > > > > > > > On Thu, Dec 3, 2015 at 5:52 PM -0800, "Douglas Greve" > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > I guess I'm not sure what you are trying to do. Can you elaborate? > > > > On 12/3/15 6:24 PM, Sabrina Yu wrote: > > > Hi Doug, > > > > > > Thanks for the quick reply. Is Xhemi only for measuring volumes for > > both hemispheres? > > > > > > > > > https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg35097.html > > > You mentioned editing pctsurfcon to set white matter and gray matter > > in this email thread here. Can this be used to measure of white matter > > intensity for lh only, and then rh only? This email thread sounded > > promising for what I need, but am also unsure of how to input set wm > > and gm commands. > > > > > > Thanks, > > > Sabrina > > > > > > ________________________________________ > > > 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: Thursday, December 3, 2015 2:31 PM > > > To: freesurfer@nmr.mgh.harvard.edu > > > Subject: Re: [Freesurfer] Left and right white matter intensity ratio > > > > > > see if this tool is what you need. It allows you to map to the > homolgous > > > vertex on the contralateral hemisphere > > > http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi > > > > > > On 12/03/2015 05:25 PM, Sabrina Yu wrote: > > >> Hi there, > > >> > > >> > > >> Would it be possible to use pctsurfcon to calculate the ratio of > white > > >> matter signal intensity between left and right hemispheres? > > >> > > >> Thank you > > >> Sabrina > > >> > > >> > > >> _______________________________________________ > > >> 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> > <http://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 mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > 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> > <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 > > > _______________________________________________ > 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
_______________________________________________ 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.
