Thank you for your answer.
I’m familiar with the preprocessing of fMRI with these softwares, however I just don’t see how I can extract these time series for each region in the xls file ? Is there a script or a software for that ?
You could try using fslmeants or mri_segstats and concatenate the ROI signals into a single file. I believe the option –avgwf of mri_segstats saves directly your ROI time series into a text file. Check the forum/websites of FSL and FreeSurfer.