Re: [Freesurfer] memory allocation error with mris_register

Try doing it in matlab, so a = MRIread('orig.mgz'); MRIwrite(a,'orig.mgz');

doug

Arno Klein wrote:

dear doug,

i am using FS v5.1 now but ran the 20 oasis subjects through FS v5.0. i am only having this trouble for one of the subjects.

after the mri_convert workaround i am still getting the same memory allocation error.

cheers, @rno

On Fri, Jan 20, 2012 at 4:23 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

This is a strange problem we've been having with some mgz files
that were generated during a short period of time last summer when
there was a bug in the mgz writing code. What version of FS are
you using? In the current dev version, this should not be a
problem. A work-around is to convert the orig.mgz to itself using
mri_convert in the dev environment, ie,

mri_convert orig.mgz orig.mgz

doug

Arno Klein wrote:


    i get the following memory allocation error for only one out
    of 20 oasis subjects that i processed with freesurfer 5.1 on
    an ubuntu 11.10 machine with 24gb memory:

    mris_register -curv subjects/OAS1_0061_MR1/surf/lh.sphere
    templates_freesurfer/lh.KKI_2.tif
    subjects/OAS1_0061_MR1/surf/lh.sphere_to_KKItemplate.reg
    using smoothwm curvature for final alignment
    $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $
     $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $
    reading surface from subjects/OAS1_0061_MR1/surf/lh.sphere...
    TAGskip: tag=1717658469, failed to calloc 1868656640 bytes!
    Cannot allocate memory

    system information:

    FREESURFER_HOME: /usr/local/freesurfer
    Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
    Debian version: wheezy/sid
    Kernel info: Linux 3.0.0-14-generic x86_64

    cheers,
    @rno

    ------------------------------------------------------------------------

    _______________________________________________
    Freesurfer mailing list
    Freesurfer@nmr.mgh.harvard.edu
    <mailto:Freesurfer@nmr.mgh.harvard.edu>
    https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


-- 
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>



The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners
Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to
you in error
but does not contain patient information, please contact the
sender and properly
dispose of the e-mail.