Dear AFNI experts,

I'm also having a similar issue. I've run the following script:

@SSwarper \
-input ${T1_data} \
-base MNI152_2009_template_SSW.nii.gz \
-deoblique_refitly \
-subid ${sub_id} \
-giant_move \
-odir $startdir/pre_warp_${sub_id}

A large portion of the anatomical image is missing after second pass skull-stripping (see attachments). Any ideas of what might be causing this?

The first pass skull-stripping seems fine. What is the difference between the first and second skull-stripping? Would it be acceptable to feed "anat.S" instead of "anat.SS" to the afni_proc?

Thank you!

All the best,
Irene