Hi Amy,

Sorry for the late reply, I believe the remaining issue is simply that subject-specific ROIs (like those we are using here, defining by FreeSurfer and located at a different location for each subject) do not have any associated unique and well-defined MNI-space coordinates. The second-level results display functions will attempt to place these ROIs at the world-coordinates specified for the first subject, but those are going to look out-of-place if the reference space of the first subject (in this case that is the space of the T1w image that was processed by FreeSurfer) is off the standard MNI-space reference. This means that your ROIs are being properly defined now, but CONN does not have a way to figure out where to locate them in MNI-space for plotting purposes. 

One way to work around this issue, which only applies to FreeSurfer-generated ROIs (not to other forms of subject-specific ROIs), is to enter in the Setup.ROIs tab instead of the aparc*+aseg.mgz files (one subject-specifc RO defining your FreeSurfer ROIs projected back into subject-space) directly the associated lh.aparc*+aseg.annot files (a single subject-independent file defining the same FreeSurfer ROIs but in fsaverage space), and then selecting the option that reads "compute average timeseries from unsmoothed volumes" (assuming that you have used CONN's surface-based pipeline, after the "functional_surface_resample" step those functional volumes would also be defined in fsaverage space). When doing this, the ROI functional data is still going to be extracted from the correct cortical locations separately for each individual subject, but now CONN is going to automatically associate with each individual ROI a set of reference MNI-space coordinates (which are only used for display purposes) defined by the position of the centroid of this ROI in the MNI-space FreeSurfer reference lh/rh.pial surface (see "conn_surf_coords.m" for details). This allows conn second-level plotting functions to use some "reasonable" MNI-space coordinates when displaying each ROI (of course, these reference coordinates are not perfectly accurate simply because in reality the coordinates of each ROI may actually be in different locations for different subjects, and also the fsaverage reference surfaces are just an approximation to where the subject-specific surfaces will be for each subject, but at least they should be reasonably indicative of the general location in MNI-space of each ROI)

Let me know if that makes sense and/or if you run into issues. 

Best
Alfonso

Originally posted by Amy Bouchard: