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 > <gr...@nmr.mgh.harvard.edu <mailto:gr...@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 > gr...@nmr.mgh.harvard.edu <mailto:gr...@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. > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
