Hi, Sungshin-
I would give @SSwarper a try on your original dataset.
It should produce a skullstripped+unifized version in the original space; a nonlinear transformation to standard space (e.g., MNI), and a representation of the brain warped to standard space. It can be a bit slow-- a couple hours on a laptop-- but if you can run on a multicore machine, you can specify the number fo threads to use (it is parallelized using OpenMP) by setting the environment variable OMP_NUM_THREADS.
Assuming you have an uptodate version of AFNI ("afni -ver" to check, "@update.afni.binaries -d" to update), you can run something like:
@SSwarper \
-input DSET_T1_ORIG \
-base MNI152_2009_template_SSW.nii.gz \
-subid SUBJ_NAME \
-odir .
... and please check the help file for more info (e.g., file names, automatic QC images made, etc.).
--pt
