Hi Tali

that's a giant defect. Almost 1/4 of the total normal surface area. Something must be seriously wrong. Check out the filled.mgz and see if the skull or cerebellum is attached to the wm.

cheers Bruce

On Fri, 6 Jul 2012, Tali Swisher wrote:

Hi all,

I'm running FreeSurfer v.4.0.5 (see below) and it keeps hanging during the Fix Topology sequence while correcting defects. The last few lines before it's hanging are included below - any suggestions?

-------- freesurfer-Linux-rh9-stable-pub-v4.0.5 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME   /share/apps/freesurfer4.0.5 FSFAST_HOME       /share/apps/freesurfer4.0.5/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR      /home/pnlstaff/freesurfer/subjects MNI_DIR           /share/apps/freesurfer4.0.5/mni ____________________________________________________________________ CORRECTING DEFECT 67 (vertices=117, convex hull=78) After retessellation of defect 67, euler #=27 (83599,243374,159802) : difference with theory (-19) = -46

CORRECTING DEFECT 68 (vertices=19, convex hull=68) After retessellation of defect 68, euler #=28 (83608,243425,159845) : difference with theory (-18) = -46

CORRECTING DEFECT 69 (vertices=38132, convex hull=10573)

Thanks! Tali

-- Talis M. Swisher, BA Senior Research Assistant Psychiatry Neuroimaging Laboratory Harvard Medical School, Brigham and Women's Hospital 1249 Boylston St, 3rd Floor Boston, MA 02215 Office: (617) 525-6119 Cell: (336) 577-5071 Fax: (617) 525-6150