afni.nimh.nih.gov

Lukas,

Try the following;

First, scalp the AFNI anatomical dataset with bet (after converting into analyze)
/usr/fsl/bin/bet MPrage.hdr EMc_scalp

Next, Put into to3d using original (unscalped) tlrc MPrage anatomy as the geometry parent:
to3d -geomparent MPrage+tlrc -prefix EMc_scalp_final2 -type anat -view tlrc EMc_scalp.hdr

That has worked for us.

Tim Souza