Hi Rick,

I'm a little confused regarding Freesurfer's usage here. I had run Freesurfer prior to @SUMA_Make_Spec_FS, where Freesurfer was used to reconstruct surfaces from T1w/T2w structural images, and the the motion-corrected functional series (after resampling to T1w space) is sampled to the surface. In total, Freesurfer is generating surfaces in the subjects' native space, and also transforming them to an fsaverage template space.

It seems to me then that using the MNI standardized anat and EPI datasets in 3dVol2Surf is incorrect, since Freesurfer was working in subjects' native space. Might it be better than to use @SUMA_AlignToExperiment where the -exp_anat option contains the T1w anatomical (skull-stripped)? Or are the fsaverage surface files appropriate in this case?

Dan