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
> <gr...@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,
>>> @rno
>>>
>>>
>>>
>>> On Fri, Jan 20, 2012 at 4:23 PM, Douglas N Greve <
>>> gr...@nmr.mgh.harvard.edu
>>> <mailto:gr...@nmr.mgh.harvard.**edu<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:freesur...@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
>>> gr...@nmr.mgh.harvard.edu
>>> <mailto:gr...@nmr.mgh.harvard.**edu<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>
>>>
>>> <http://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>
>>>
>>> <http://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<http://www.partners.org/complianceline>.
>>> If the e-mail was sent to
>>> you in error
>>> but does not contain patient information, please contact the
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>>> dispose of the e-mail.
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>>>
>> --
>> 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<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>
>>
>>
>
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