No, don't try to register them directly to fsaverage. Create a registration matrix for each 1st level (sounds like you've done this), then use mri_vol2surf with "--trgsubject fsaverage". This will sample the CON to the subject's individual surface, then use the surface-based registration to map to fsaverage.

doug

Andrew Jahn wrote:

Hi all,

I am interested in using Freesurfer to project volume data onto the inflated brains run through the FS pipeline. I am using SPM and have been able to project 1st level con and spmT images onto the corresponding subject's inflated anatomical.

My question is, if I wanted to look at 2nd level SPM results on an inflated brain, would it make the most sense to project them onto fsaverage? For example,

spmregister --s fsaverage --mov spmT_0001.hdr --reg register.dat

Or, is there a way to average the surfaces of the subjects in the study and then project their second levels onto that averaged surface?

Thanks!

-Andrew

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