Hi Negar, sorry about the delay. The first thing to do is to look at the orig.mgz to see if there is anything funny going on, maybe most of the image is dark with one very bright spot or some other distortion. If that looks ok, please tar up the subject and drop it to me at our file drop (url at thenend of this email). doug
On 11/26/2012 09:10 PM, Negar Memarian wrote:
Hello Dr. Greve, I'm not sure if my questions actually get posted on the FreeSurfer email list or not, as I have never received a reply. I really need help with the following issue and would appreciate if you or your colleagues please advise: **I've checked similar posts on the email-list and still could not find an answer to my question. I'd really appreciate your attention and feedback: recon-all -autorecon1 crashes for me in one of the steps before skull stripping with an error like this: Done spline_smooth: posixio.c:210: px_pgin: Assertion `*posp== ((off_t)(-1)) || *posp== lseek(nciop->fd, 0, 1)' failed. nu_estimate_np_and_em: crashed while running spline_smooth(termination status=6) nu_correct: crashed while running nu_estimate_np_and_em(termination status=65280) ERROR: nu_correct Linux FreeSurfer2.6.28-11-generic #42-UbuntuSMPFri Apr 17 01:57:59 UTC2009 i686GNU/Linux recon-all -s BT501_FSexited with ERRORS at Mon Nov 26 15:26:10 EST2012 I made sure that I have the newest version of FreeSurfer, the environment variables MNI_DATAPATH and MNI_PERL5LIB and PERL5LIB exist and I ran $FREESURFER_HOME/bin/fixup_mni_paths as well. But unfortunately I still face the same problem. I also tried the process for a different subject, but the same error. Does anyone have any idea how I can fix this? I have attached the recon-all.log file. I'd really appreciate your help. Negar Negar Memarian, MASc, PhD NSERC Postdoctoral Fellow Department of Neurology David Geffen School of Medicine at UCLA