@SSwarper - problem with skullstripping

Dear AFNI users,

I have problems with running @SSwarper on T1 data (T1 MPRAGE). I’ve run the script on 5 images and it worked perfect, but on 6th not :frowning: It seems that top of brain is cut when creating anat.SS file (anat.S is fine!). I enclose printscreens.
I already updated afni binaries and it did not help. No idea what went wrong… I will be grateful for help.


As a test, try running @Align_Centers on the input anatomical dataset first and report back with the actual @SSwarper command using the shifted anatomical and the outcome.