3dSkullStrip results

Dear AFNI users,

Parts of the pons and brainstem were chopped off after 3dSkullStrip (see the attached). Is there a way to be less stringent in skull stripping?



If you are also doing nonlinear warping to MNI space, then you can use the @SSwarper script, as in

@ SSwarper anat_sub007+orig sub007

Read the output of @SSwarper -help for the details

If you are NOT doing nonlinear warping, then the output of 3dSkullStrip -help has a bunch of information on how to make the skull stripping more or less strict.