Dear Alfonso,

Thank you for clarifying my questions. This saved my day!

Sincerely,
Michelle

Originally posted by Alfonso Nieto-Castanon:

Dear Michelle,

You are exactly right, you should point these volume-level ROIs to extract BOLD signal from your "subject-space functional data" dataset (or any other appropriate volume-level functional data file). In general when running surface-level analyses, and possibly mixing volume- and surface- level ROIs or data files, each individual ROI should point to the appropriate (same-space / same-level) BOLD signal source (this of course also applies to those cases when one is running volume-level analyses but is mixing ROIs across different spaces, e.g. some ROIs in MNI-space and others in subject- space). In your case that means pointing the Gray/White/CSF ROIs to the extract the BOLD signal from those same functional files but without the ".surf" in the filename.

Hope this helps

Alfonso

Originally posted by Michelle Cheng:

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