can you load the lh.sphere in tksurfer? I'm not sure it is the mgz file that is the problem. Maybe your partition filled up and the sphere file isn't complete?
On Fri, 20 Jan 2012, Arno Klein wrote:
dear doug, sadly, no dice.
cheers, @rno
On Fri, Jan 20, 2012 at 4:45 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote: 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, @rnoOn 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
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