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