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 <greve@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
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