There is a bug in today's stable4 build that affects reading mgh/mgz volumes. I've checked in a fix. It should be fine by tomorrow.
On Thu, 2007-10-04 at 16:27 -0400, Help Desk -- Paul Raines wrote:
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
What computer are you getting the error on, is it running CentOS5 ?
Pratap Kunwar wrote:
I am also getting the same error as below.
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