There is vertex-for-vertex correspondences, but that does not mean that each subject aligns perfectly. There maybe some subjects where a vertex is in the medial wall but not for another subject. They are close, but not in perfect alignment. What I would do is something like this:
a = [subject1fmri.vol(:,:,:,1); subject2fmri.vol(:,:,:,1); subject3fmri.vol(:,:,:,1); ...]; b = a>0; mask = mean(b)==nsubjects; On 09/28/2016 05:58 PM, Dorothy Sincasto wrote: > Hi Douglas, > > Thanks for your reply. > > I thought when individual space data is projected onto fsaverage5 > space it get wrapped in a common space, so one vertex would correspond > to the same area across subjects, like in MNI. > > I tried to create a group subcortical mask by loading each subject > fmri surface and selecting the vertex with zero-values and adding one > to corresponding element in the 20484 vector . In percentage, 62 > vertices are non-zero in half or more of the data size, and 106 in 40% > or more. In average, each subject has 120 zero-valued vertices. > > If I don't want to account for non-cortical activity in my analysis, > do you consider a good approach to discard this 106 vertices that at > least in 40% of the subjects are non cortical? > > Thanks, > Dorothy > > > On Wed, Sep 28, 2016 at 12:37 PM, Douglas Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > It is changing with each subject because each subject's brain is > different, and you can't get a subject-specific mask from > fsaverage5. Can you load all your data into matlab and then > compute a mask based on non-zero voxels? > > > On 9/28/16 1:57 PM, Dorothy Sincasto wrote: >> Hi freesurfers, >> >> I am doing a connectivity analysis on cortical areas. I load the >> 2d fmri surface file in fsaverage5 space into matlab and I get >> 20484 vertices for both hemispheres. Some of which are zero >> because I previously specified to get only the cortex vertices. >> However, the number of non-cortex vertices changes across subjects. >> >> Is it possible to get from fsaverage5 any overlay mask that >> specifies if it is cortical or not, so when I load it into matlab >> i can get a logical vector of 20484 elements? >> >> Thanks >> Dorothy >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > _______________________________________________ Freesurfer mailing > list Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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 > <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
