Dear all,

I'm trying to connect fmri and mri data. For that I've used FreeSurfer for subcortical segmentation and now I want to create a roi-to-roi analysis for both surface based and subcortical volumes (the ones from FreeSurfer). I've read that both subcortical and surface-based cortical parcellations can not be combined in the same analysis. Is this still the case or in other words, how can I perform roi-to-roi analysis for both surface based and subcortical volumes?

This post suggests that it is possible but I'd like to make sure. Hence, define my T1 files from Freesurfer in as well as my functional images. Run the default surface-space preprocessing pipeline in CONN. After that select my subject-specific subcortical (for example: aseg+aparc.mgz) parcellation FreeSurfer files and then select the option that reads 'extract from secondary dataset'. Click on Done and proceed to the first level analysis where I specify my roi-to-roi analysis?

Thank you, dear list! 

Tom