Hi Negar, I cannot reproduce this error. I'm not sure how to proceed, but here are three possibilities:

1. Is this a virtual machine? If so, do you have a real machine you can run it on? 2. You only have 2G of memory on your machine. Can you increase that or run it on a machine with more? 3. There is an outside chance it could be an MNI version issue. Run nu_estimate_np_and_em and look at the version (should be 1.10)

doug

On 11/27/2012 03:31 PM, Negar Memarian wrote:

Hi Doug,

Thanks very much for your reply. I checked the org.mgz and it looks okay, so as you advised I uploaded the subject to FileDrop for you to see. I also uploaded the recon-all log file so you can see where exactly the error occurs.

Many thanks and looking forward to hear from you, Negar

On Tue, Nov 27, 2012 at 9:42 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

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


-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 <tel:617-724-2358>
Fax: 617-726-7422 <tel:617-726-7422>

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/



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