a feature in the new freeview that helps with this is to load the ?h.orig.nofix then load the ?h.defect_labels as an overlay on it, and check the "use surface overlay" box when selecting the color of the surface. This will color regions of the surface that are in a defect differently than the non-defective surface, which is very, very handy for understanding what's going on with a defect (thanks Ruopeng!)

cheers Bruce

On Fri, 10 Mar 2017, Falk Lüsebrink wrote:

Dear Andrius,

You can load the ?h.inflated.nofix in freeview and the overlay ?h.defect_labels to see what's going on. It may be that a chunk of skull or the cerebellum is still attached, in which case you'll want to correct the brainmask.mgz or wm.mgz, respectively, to remove the non-brain tissue.

Best,

Falk

Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Andrius Gesendet: Freitag, 10. März 2017 10:06 An: freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] FS v6.0 recon-all freezes

Hi,

Maybe some could give advice regarding my problem with FS v6.0.

Now I am running recon-all for my patients cohort on Linux Centos 6, FS v6.0. It is PC with i5 intel, 4 Core, 8 Gb RAM. 80% of my subjects finished recon-all process without errors pretty fast (it takes about 11-14 hours per subject). But about 20% subjects hang at the same point of recon all :

#@# Fix Topology Copy lh Wed Mar  8 11:22:47 EET 2017 #@# Fix Topology Copy rh Wed Mar  8 11:22:47 EET 2017 #@# Fix Topology lh Wed Mar  8 11:22:47 EET 2017 #@# Fix Topology rh Wed Mar  8 11:22:47 EET 2017

It hangs for infinity at this point. Tried to do it on other PC with same parameters but it stucks at the same point.

Any ideas what is wrong?

Thank you very much

Andrius