Dear CONN experts,

I have preprocessed a dataset using the "preprocessing pipeline for surface-based (in subject-space) using nonlinear coregistration." The structural images were brain.mgz files generated by FreeSurfer and aseg.mgz files were also incorporated. After the preprocessing, I noticed in the "Setup > ROIs" section that the gray matter, white matter, and CSF (c{1,2,3}_aseg.img respectively) were all pointed to "unsmoothed functional data (secondary dataset #1)." In the "Setup > Other imaging data" section, those unsmoothed functional data pointed to ww*.surf.nii, which I assume were functional data resampled on the cortical surface. Now my questions are:

1) Can I go ahead with this automatic configuration? Does CONN try to extract CSF signals from the cortical surface (!?) or automatically identify the corresponding volume-based functional data and extract the signal therein?

2) Or should I manually point the GM/WM/CSF ROIs to "subject-space functional data" also generated by the pipeline (ww*.nii with no "surf" in the file name) available in the Other imaging data section?

Thanks in advance for your help!

Sincerely,
Michelle