Hi Bruce,
Thanks for the tip on bert, I tried running the compiled version of mri_em_register on fsaverage and it seems to run without giving the error. I've been scavenging through the fswiki to find the latest version of bert but to no success.. could you maybe help me find the url to it?
Thanks very much!
Danny Kim Children's Brain Mapping Centre BC Children's Hospital ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, October 24, 2012 4:21 PM To: Kim, Daniel Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] znzTAGskip error using mri_em_register
Hi Danny
try downloading a new version of bert. This was a bug we had briefly but fixed a while ago. Maybe you got a version of bert that was generated with it?
cheers Bruce On Wed, 24 Oct 2012, Kim, Daniel wrote:
Hello FreeSurfer users,
I was finally able to compile mri_em_register successfully from source and trying to test the build with subject 'bert', I ran into this error
~/freesurfer/bin# ./mri_em_register -uns 3 -mask $SUBJECTS_DIR/bert/mri/brainmask.mgz $SUBJECTS_DIR/bert/mri/nu.mgz $FREESURFER_HOME/average/RB_all_2008-03-26.gca $SUBJECTS_DIR/bert/mri/transforms/talairach.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 3 using MR volume /usr/local/freesurfer/subjects/bert/mri/brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer_4_5_0/freesurfer/average/RB_all_2008-03-26.gca'... average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading '/usr/local/freesurfer/subjects/bert/mri/nu.mgz'... znzTAGskip: tag=-8454144, failed to calloc 4286513152 bytes!
Cannot allocate memory
Has anyone had similar error before?
I'm using Ubuntu 10.04 LTS- 64 bit and I've built mri_em_register from scratch using CVS public checkout "-P dev" The test subject was through installing freesurfer 5.1.0 and also same has happened with freesurfer 4.5.0
Any help with this would be again greatly appreciated!
Cheers!
Danny Kim
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