Hi all,
I've installd FreeSurfer through Xubuntu virtual machine on Windows 7, 64 bit according to the installation instructions the FreeSurfer Beginner's Guide. Unfortunately I'm facing an error in the recon-all process (as described below), which I think has to do with the VM, because the error does not occur if run on a real Linux machine. Would someone please advise if I'm missing something? Are there specific VM setup steps in terms of sharing drives or copying certain files into a specific folder that I'm not aware of? (I have just followed the steps on the installation guide, nothing more).
The problem I'm facing is:
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 FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC2009 i686GNU/Linux recon-all -s BT501_FS exited with ERRORS at Mon Nov 26 15:26:10 EST 2012
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