Okay, so it is not just CentOS5. But the timestamp on the build is TODAY. So I guess we wait for someone from the freesurfer development team to say something about what changed.

On Thu, 4 Oct 2007, Pratap Kunwar wrote:

Yes, here is the info below

FREESURFER_HOME: /usr/local/freesurfer/stable4

Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.0.1-20071004

RedHat release: CentOS release 4.4 (Final)

Kernel info: Linux 2.6.9-42.0.3.ELsmp x86_64

NMR Center info (/space/freesurfer exists):

machine: galen

SUBJECTS_DIR: /autofs/space/galen_002/users/carl/S4_HR_LR18/S4_HR_LR18_recon/

PWD: /autofs/space/galen_002/users/carl/S4_HR_LR18/S4_HR_LR18VvI

Pratap Kunwar pkunwar@nmr.mgh.harvard.edu

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What computer are you getting the error on, is it running CentOS5 ?

Pratap Kunwar wrote:

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I am also getting the same error as below.

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Hi Chris,

Can you forward me to the person I could ask about this issue?

I've been running jobs the same way using freesurfer for months and today I keep gettting this error message: Cannot allocate memory

i.e. mri_convert orig.mgz ./tmp.mri_nu_correct.mni.29819/nu0.mnc mri_convert orig.mgz ./tmp.mri_nu_correct.mni.29819/nu0.mnc TAGskip: failed to calloc 808464384 bytes! $Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $ reading from orig.mgz... Cannot allocate memory ERROR: converting to minc Linux madrc 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:39:17 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Thu Oct 4 13:35:24 EDT 2007

i.e. reading '/usr/local/freesurfer/stable4/average/RB_all_2007-08-08.gca'... average std = 6.7 using min determinant for regularization = 4.5 0 singular and 1985 ill-conditioned covariance matrices regularized reading 'nu.mgz'... TAGskip: failed to calloc 842542592 bytes! Cannot allocate memory Linux madrc 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:39:17 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Thu Oct 4 13:40:14 EDT 2007

Is there something I can do to fix this problem? Thanks! ~Amy

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On Thu, 4 Oct 2007, Amy DeLuca wrote:

  You cab subscribe your self at this URL

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Can you plese add me to the freesurfer email list?

Freesurfer Jobs are constantly exiting giving me this error: Cannot allocate memory Thank You

~amy

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Chris Johnson |Internet: johnson@nmr.mgh.harvard.edu Systems Administrator |Web: http://www.nmr.mgh.harvard.edu/~johnson NMR Center |Voice: 617.726.0949 Mass. General Hospital |FAX: 617.726.7422 149 (2301) 13th Street |Fifty percent of all doctors graduated in the Charlestown, MA., 02129 USA |lower half of the class. Observation

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