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> 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 > listfreesur...@nmr.mgh.harvard.eduhttps://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. > >
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