Hi Arno, Please give these matlab commands a shot.
[v,M, mr] = load_mgh('orig.mgz'); save_mgh(v, 'orig.mgz', M, mr);
-Louis
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.eduwrote:
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 < greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@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<Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://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/**compliancelinehttp://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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html