Dear all,
I just wanted to double-check if I am doing the right thing.

I am transferring fMRI data from FSL to the surface in Freesurfer to test whether cortical thickness is related to BOLD signal change.

I used the steps described here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer

I did the following:
1) I carried out Freesurfer reconstruction for all subjects
2) I performed 1st level analysis for fMRI data in FSL, separately for each run, without smoothing
3) Then I obtained good registration of FEAT example_func of each run to the subject's anatomical using FLIRT. This I have done already for a specific contrast of interest.
The above steps have been performed with Freesurfer version earlier than 5.0. Will there be a problme if I continue the steps below with the newest stable version?
Now I plan:
4) Combine the 3 runs/subject on the surface by averaging them with smoothing. As this is within-subject, my guess is that 5mm will be the best.
5) Concatenate the images for all subjects to perform analyses

I am not sure about the following points:
- what are the units of the zstat images transferred onto the surface? Is it still the logarithmic scale as for thickness analyses?
- I will want to create a fMRI-based ROI and then investigate the thickness especially within this region. i know I can extract mean ROI values and use other statistical software, but how can I perform vertex-wise analysis within this ROI? I assume qdec does not allow this, so only the DODDS analysis is possible.

Thank you a lot for your support!
Best,
Aga