I have been using Freesurfer v5.3 to perform surface reconstruct for 1mm isotropic T1 (MPRAGE) and T2 (SPACE) weighted images from a Siemens 3T Trio scanner with a 32-channel head coil. Unfortunately for half of my subjects I receive an rather odd pial surface artefact, while the 'white' surfaces do not suffer from the same issue.

The command line I have used was:

recon-all -all -subjid <subjectid> -T2  <subjectdir>/mri/orig/T2.mgz -T2pial -3T

Are you familiar with this issue and do you have some advice for me?

Thank you very much for your help.