The coords in the summary file are for the white surface, not the inflated. Try freeview again using the white surface
On 04/29/2014 07:50 AM, Rujing Zha wrote: > Hi doug, > Thanks doug. > I saw the sig.mgh in freeview by typing this: > freeview -f > $SUBJECTS_DIR/fsaverage/surf/rh.inflated:annot=aparc.annot:overlay=./sig.mgh > I set the vertex number which is at the maxmum in freeview. And the > "pic1" in the attachment displays the cluster information in the > *.summary file. "pic2" in the attachment represents freeview snapshot. > The arrow in these two files echo the different coordinates which is > refered in the previous e-mail. > Thanks again. > All the best. > Rujing Zha > > > > > > At 2014-04-29 02:46:07,"Douglas N Greve" <gr...@nmr.mgh.harvard.edu> wrote: > > > >On 04/26/2014 07:06 AM, charujing123 wrote: > >> Hi all, > >> I have done group analysis and see it in freeview. Also I can see my > >> sig.cluster.summary file to find clusters those survived. As I know, > >> the MNIX MNIY MNIZ in the cluster summary file is coordinates for the > >> maximum. The coordinate system is MNI305. Also I input the vertex > >> number at the maximum in freeview, but it echo different coordinate > >> for the vertex from that in cluster summary file. Why? > >Which coordinate? are you looking at and on which surface? > >> Another question. There is "RAS" symbol at the bottom of freeview > >> window. However I see the coordinates : inferior, posterior, left is > >> negtive, superior, anterior,and right is positive. I suspect the > >> coordinate system is LPI. Is that right? > >If left is negative, then it is RAS > >> Thanks. > >> All the best. > >> Rujing Zha > >> 2014-04-26 > >> ------------------------------------------------------------------------ > >> charujing123 > >> > >> > >> _______________________________________________ > >> 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 > > > > > >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. > > > > > > pic1.jpg > > > > pic2.jpg > > > > > _______________________________________________ > 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
