[Freesurfer] Two timepoints - same subject, correlation matrix

Hi,

Can somebody please help me figure out how to correct this issue?

1 subject - 2 functional scans

1) run recon-all on subject anatomical.

2) process functional series (using AFNI/FSL) - each individually.

3) use (http://afni.nimh.nih.gov/pub/dist/doc/program_help/@ROI_Corr_Mat.html) @ROI_Corr_Mat -ts proc_func1 -roi aparc+aseg -prefix all (each individually)

This works (I don't know why since I am not doing anything to register them to a common space).

4) I get a square matrix of 109 (n x n correlation matrix) in 1 timepoint and 112 in 2nd timepoint.

I would like to get the exact same number so I can compare them! Of course I can manually adjust the rows/columns later, but I am not sure this is the smartest way to do this.

Can I do all the steps in Freesurfer?

Thank you, S