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
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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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.eduwrote:
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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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.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 greve@nmr.mgh.harvard.edu <mailto:greve@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.
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
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
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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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@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 greve@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
dear bruce,
you're right -- i am able to view the pial surface, but when i try to view the spherical surface with tksurfer i get the same memory error.
is there any way to fix the sphere without affecting anything else? neuromorphometrics has painstakingly manually edited the freesurfer labels generated for this subject and i don't want to introduce any alterations to the meshes that they labeled.
cheers, @rno
On Fri, Jan 20, 2012 at 5:30 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
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?
you can just rerun the mris_sphere command that is in the recon-all.log (or recon-all.cmd)
cheers Bruce On Fri, 20 Jan 2012, Arno Klein wrote:
dear bruce, you're right -- i am able to view the pial surface, but when i try to view the spherical surface with tksurfer i get the same memory error.
is there any way to fix the sphere without affecting anything else? neuromorphometrics has painstakingly manually edited the freesurfer labels generated for this subject and i don't want to introduce any alterations to the meshes that they labeled.
cheers, @rno
On Fri, Jan 20, 2012 at 5:30 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: 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?
thank you -- this worked!
cheers, @rno
On Fri, Jan 20, 2012 at 6:43 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
you can just rerun the mris_sphere command that is in the recon-all.log (or recon-all.cmd)
cheers Bruce
On Fri, 20 Jan 2012, Arno Klein wrote:
dear bruce, you're right -- i am able to view the pial surface, but when i try to view the spherical surface with tksurfer i get the same memory error.
is there any way to fix the sphere without affecting anything else? neuromorphometrics has painstakingly manually edited the freesurfer labels generated for this subject and i don't want to introduce any alterations to the meshes that they labeled.
cheers, @rno
On Fri, Jan 20, 2012 at 5:30 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote: 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?
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.
freesurfer@nmr.mgh.harvard.edu
-
Arno Klein -
Bruce Fischl -
Douglas N Greve -
Louis Nicholas Vinke