I am using freesurfer to run recon-all,  recon-all -i T1_MPRAGE image  -t2  T2-FLAIR-Image    It takes about 5 days to finish the process.   I find that the most time consuming process is topology fix,  it almost takes 4 days for L and R side of hemisphere.    I checked the manual,  it is supposed to take 1-9h to finish.   Do you know why?   I think my data set may have a relatively large ventricles ( of course, it is not so large). I put the flags --bigventricles and --parallel,  it still takes about 3 days to finish.  

but if I use  recon-all -i T1_MPRAGE image rather than recon-all -i T1_MPRAGE image -t2 T2-FLAIR-Image.   It will take about 15h, why this make such big difference? 

Many thanks.

Frank