Thanks for getting back to me. I have a few more questions:
What sort of registration should I be doing to get my regions into BS space?
We are trying to confirm our findings from Freesurfer in a separate analysis stream. So we will have both a Freesurfer based reconstruction and a Brain Suite based reconstruction for each participant. The end goal is to extract the thickness values for each region that we are interested in. All of our regions are hand drawn in Freesurfer as labels which we can convert to volumes (.nii) easily enough. Should I be registering their Freesurfer based anatomy to one of the outputs from the ‘Cortical surface extraction sequence’? If so, which output should I aim for.
I hope the above was clear. Please let me know if you need additional info.