Hi Linda

napo4128: something is wrong with the 001.mgz. How did you create it? The direction cosines definitely shouldn't have a 0 determinant

napo0195: this is new error for me. The topology fixing couldn't find a correct solution. If you upload the subject we'll see if we can replicate and fix this problem

napo4252: I've never seen this before either - mris_make_surfaces segfaulting right away. Maybe you ran out of disk space and one of the volumes/surfaces it needs is corrupted? Try running it by itself:

setenv SUBJECTS_DIR /home/virtualuser/freesurfer/lindadata/subjects mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs napo4252 lh

and see if it happens again. If so, I guess I would go through all the volumes and surfaces and make sure that they are visually reasonable in tksurfer/tkmedit/freeview. If that doesn't reveal something, then upload this one as well

cheers Bruce

On Fri, 14 Jun 2013, Linda Zhang wrote:

Dear all,

I've been running recon-all (subj) -all for a group of subjects on Freesurfer v5.1.0 on Virtualbox. Three of them exited with errors, each one having a different error. I've attached the recon-all.logs. For napo0195, the problem may be with the wm.mgz as someone mentioned before, but I don't know what the issue might be for the other two subjects. Thanks for your help!

Cheers, Linda