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?
Thanks.
ping
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.