Hi Daniel,

Thank you so much for your guidance! I have finally figured out how to edit the skull-stripped volume/mask and tried some other things, but have a couple of follow-up questions.

For editing the skull-stripped volume/mask, should I use anatS.subID.nii (first pass skull-stripped output) or anatSS.subID.nii (second pass skull-stripped output)? Also, I couldn’t figure out how to feed the fixed/edited volume/mask back into a 2nd run through of @SSwarper to solve the skull-strip problem. Could you please give me some guidance on how to properly do that?

I tried the following ways but none of them worked. 1) After getting the edited skullstripped volume, I tried using that as an input for @SSwarper and added the “-init_skullstr_off” option; 2) I also tried using the “-mask_ss MSS” option and supplied an edited skull-stripped mask (as well as a skull-stripped mask using FSL). But both of these options seem to give me the exact same result/skull-strip problems. I guess this might be because both of these options only apply to the first-pass of skull-stripping (per the AFNI help guide)? (Is there a way to turn-off or skip the second pass of skull-stripping? I think the answer is no and probably would defeat the purpose of @SSwaprer, but just out of curiosity...)

One more thing that I tried is to skull-strip this particular participant through FSL and use the output volume as an input for afni.proc.py and skip the @SSwarper step. In the afni.proc.py script, I just let "-tlrc_NL_warp" do its job and grayed out "-tlrc_NL_warped_dsets". This seems to help. Is this also an acceptable way of solving the problem?

Thank you so much for your patience!