Hi, Yasir-

One quick thought---WMe is never defined there, which I guess would typically be a follower dset of some kind.

Note, re. the speed of FreeSurfer---if you check this tutorial page about it, the "-parallel" option does speed things up a lot, if you have, say, 4 CPUs it can use on your computer:
[afni.nimh.nih.gov]
The "B" case there is:

# example B: using default parallelization
recon-all                                  \
    -all                                   \
    -3T                                    \
    -sd      .                             \
    -subjid  FT                            \
    -i       FT_anat_cp.nii.gz             \
    -parallel

... and it took just over 2 hours to run. That might be worth considering. Then you could use the follower dsets from 11b, too, which will likely be better tissue maps for each subject. And you *really* don't want the WM map, say, to overlap with your dataset's GM (hence the erosion of those dsets).

--pt