External Email - Use Caution
Hi FreeSurfer Developers,
I was running recon-all and it stoped at smooth1. The command is: recon-all -i T1image.nii.gz -s subject_name -all
Below is error message on the screen: #@# Smooth1 lh Mon Aug 20 23:51:55 EDT 2018 /Volumes/AERS_BACKUP/Data/OSA/FREESURFER/OSA_048/scripts \n mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix \n setting seed for random number generator to 1234 mris_smooth(27701,0x7fffec01b3c0) malloc: *** mach_vm_map(size=13835344293369151488) failed (error code=3) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug TAGskip: tag=-8454144, failed to calloc 4286513152 bytes!
Cannot allocate memory Darwin lspfis-imac.uphs.upenn.edu 16.7.0 Darwin Kernel Version 16.7.0: Fri Apr 27 17:59:46 PDT 2018; root:xnu-3789.73.13~1/RELEASE_X86_64 x86_64
recon-all -s OSA_048 exited with ERRORS at Mon Aug 20 23:51:55 EDT 2018
Although the message looks like the shortage of memory, it could run a few weeks ago. So, I really doubt memory is the main reason (the physical memory is 40GB)...The only difference before and after I can run is I reinstall the same version of Matlab 2016b by accident. Do you think I have to change some setting to run it?
Also, I've looked for solutions and couldn't find a one which really fits my problem. Would you please help me trouble-shoot this issue? Thank you so much.
1) FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 2) Platform: macOS Sierra version 10.12.6, with physical memory 40GB 3) uname -a: Darwin lspfis-imac.uphs.upenn.edu 16.7.0 Darwin Kernel Version 16.7.0: Fri Apr 27 17:59:46 PDT 2018; root:xnu-3789.73.13~1/RELEASE_X86_64 x86_64 4) recon-all.log: see attached
Best,
PH
It looks like a corrupted file. Try renaming/deleting lh.orig.nofix, regenerating it, then seeing if mris_smooth works.
On 08/22/2018 10:44 AM, Paysing Wu wrote:
External Email - Use Caution
Hi FreeSurfer Developers,
I was running recon-all and it stoped at smooth1. The command is: recon-all -i T1image.nii.gz -s subject_name -all
Below is error message on the screen: #@# Smooth1 lh Mon Aug 20 23:51:55 EDT 2018 /Volumes/AERS_BACKUP/Data/OSA/FREESURFER/OSA_048/scripts \n mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix \n setting seed for random number generator to 1234 mris_smooth(27701,0x7fffec01b3c0) malloc: *** mach_vm_map(size=13835344293369151488) failed (error code=3) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug TAGskip: tag=-8454144, failed to calloc 4286513152 bytes!
Cannot allocate memory Darwin lspfis-imac.uphs.upenn.edu http://lspfis-imac.uphs.upenn.edu 16.7.0 Darwin Kernel Version 16.7.0: Fri Apr 27 17:59:46 PDT 2018; root:xnu-3789.73.13~1/RELEASE_X86_64 x86_64
recon-all -s OSA_048 exited with ERRORS at Mon Aug 20 23:51:55 EDT 2018 Although the message looks like the shortage of memory, it could run a few weeks ago. So, I really doubt memory is the main reason (the physical memory is 40GB)...The only difference before and after I can run is I reinstall the same version of Matlab 2016b by accident. Do you think I have to change some setting to run it?
Also, I've looked for solutions and couldn't find a one which really fits my problem. Would you please help me trouble-shoot this issue? Thank you so much.
- FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
- Platform: macOS Sierra version 10.12.6, with physical memory 40GB
- uname -a: Darwin lspfis-imac.uphs.upenn.edu
http://lspfis-imac.uphs.upenn.edu 16.7.0 Darwin Kernel Version 16.7.0: Fri Apr 27 17:59:46 PDT 2018; root:xnu-3789.73.13~1/RELEASE_X86_64 x86_64 4) recon-all.log: see attached
Best,
PH
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Douglas,
Yes, I did try similar way to see if it worked. I deleted the whole folder and re-ran it. It stoped at the same place. Is there any other suggestion I could try?
Thanks,
PH
On Wed, Aug 22, 2018 at 1:23 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
It looks like a corrupted file. Try renaming/deleting lh.orig.nofix, regenerating it, then seeing if mris_smooth works.
On 08/22/2018 10:44 AM, Paysing Wu wrote:
External Email - Use CautionHi FreeSurfer Developers,
I was running recon-all and it stoped at smooth1. The command is: recon-all -i T1image.nii.gz -s subject_name -all
Below is error message on the screen: #@# Smooth1 lh Mon Aug 20 23:51:55 EDT 2018 /Volumes/AERS_BACKUP/Data/OSA/FREESURFER/OSA_048/scripts \n mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix \n setting seed for random number generator to 1234 mris_smooth(27701,0x7fffec01b3c0) malloc: *** mach_vm_map(size=13835344293369151488) failed (error code=3) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug TAGskip: tag=-8454144, failed to calloc 4286513152 bytes!
Cannot allocate memory Darwin lspfis-imac.uphs.upenn.edu http://lspfis-imac.uphs.upenn.edu 16.7.0 Darwin Kernel Version 16.7.0: Fri Apr 27 17:59:46 PDT 2018; root:xnu-3789.73.13~1/RELEASE_X86_64 x86_64
recon-all -s OSA_048 exited with ERRORS at Mon Aug 20 23:51:55 EDT 2018 Although the message looks like the shortage of memory, it could run a few weeks ago. So, I really doubt memory is the main reason (the physical memory is 40GB)...The only difference before and after I can run is I reinstall the same version of Matlab 2016b by accident. Do you think I have to change some setting to run it?
Also, I've looked for solutions and couldn't find a one which really fits my problem. Would you please help me trouble-shoot this issue? Thank you so much.
- FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
- Platform: macOS Sierra version 10.12.6, with physical memory 40GB
- uname -a: Darwin lspfis-imac.uphs.upenn.edu
http://lspfis-imac.uphs.upenn.edu 16.7.0 Darwin Kernel Version 16.7.0: Fri Apr 27 17:59:46 PDT 2018; root:xnu-3789.73.13~1/RELEASE_X86_64 x86_64 4) recon-all.log: see attached
Best,
PH
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
what version of FS are you using? I think this is a bug that we had years ago for only a few weeks. One workaround would be to load each .mgz volume into matlab and write them back out (which will strip all the tags from them). I'm not sure why you are having the problem though Bruce
On Wed, 22 Aug 2018, Paysing Wu wrote:
External Email - Use Caution
Hi Douglas, Yes, I did try similar way to see if it worked. I deleted the whole folder and re-ran it. It stoped at the same place. Is there any other suggestion I could try?
Thanks,
PH
On Wed, Aug 22, 2018 at 1:23 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote: It looks like a corrupted file. Try renaming/deleting lh.orig.nofix, regenerating it, then seeing if mris_smooth works.
On 08/22/2018 10:44 AM, Paysing Wu wrote: > > External Email - Use Caution > > Hi FreeSurfer Developers, > > I was running recon-all and it stoped at smooth1. The command is: > recon-all -i T1image.nii.gz -s subject_name -all > > Below is error message on the screen: > #@# Smooth1 lh Mon Aug 20 23:51:55 EDT 2018 > /Volumes/AERS_BACKUP/Data/OSA/FREESURFER/OSA_048/scripts > \n mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix > ../surf/lh.smoothwm.nofix \n > setting seed for random number generator to 1234 > mris_smooth(27701,0x7fffec01b3c0) malloc: *** > mach_vm_map(size=13835344293369151488) failed (error code=3) > *** error: can't allocate region > *** set a breakpoint in malloc_error_break to debug > TAGskip: tag=-8454144, failed to calloc 4286513152 bytes! > > Cannot allocate memory > Darwin lspfis-imac.uphs.upenn.edu <http://lspfis-imac.uphs.upenn.edu> > 16.7.0 Darwin Kernel Version 16.7.0: Fri Apr 27 17:59:46 PDT 2018; > root:xnu-3789.73.13~1/RELEASE_X86_64 x86_64 > > recon-all -s OSA_048 exited with ERRORS at Mon Aug 20 23:51:55 EDT 2018 > Although the message looks like the shortage of memory, it could run a > few weeks ago. So, I really doubt memory is the main reason (the > physical memory is 40GB)...The only difference before and after I can > run is I reinstall the same version of Matlab 2016b by accident. Do > you think I have to change some setting to run it? > > Also, I've looked for solutions and couldn't find a one which really > fits my problem. Would you please help me trouble-shoot this issue? > Thank you so much. > > 1) FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c > 2) Platform: macOS Sierra version 10.12.6, with physical memory 40GB > 3) uname -a: Darwin lspfis-imac.uphs.upenn.edu > <http://lspfis-imac.uphs.upenn.edu> 16.7.0 Darwin Kernel Version > 16.7.0: Fri Apr 27 17:59:46 PDT 2018; > root:xnu-3789.73.13~1/RELEASE_X86_64 x86_64 > 4) recon-all.log: see attached > > > Best, > > PH > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
External Email - Use Caution
Hi Bruce,
This is the FS version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c I reinstalled the MATLAB. Do you think this will result in the issue?
Thanks,
PH
On Wed, Aug 22, 2018 at 4:12 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
what version of FS are you using? I think this is a bug that we had years ago for only a few weeks. One workaround would be to load each .mgz volume into matlab and write them back out (which will strip all the tags from them). I'm not sure why you are having the problem though Bruce
On Wed, 22 Aug 2018, Paysing Wu wrote:
External Email - Use CautionHi Douglas, Yes, I did try similar way to see if it worked. I deleted the whole
folder and re-ran it. It stoped
at the same place. Is there any other suggestion I could try?
Thanks,
PH
On Wed, Aug 22, 2018 at 1:23 PM Douglas N. Greve dgreve@mgh.harvard.edu
wrote:
It looks like a corrupted file. Try renaming/deletinglh.orig.nofix,
regenerating it, then seeing if mris_smooth works. On 08/22/2018 10:44 AM, Paysing Wu wrote: > > External Email - Use Caution > > Hi FreeSurfer Developers, > > I was running recon-all and it stoped at smooth1. The command is: > recon-all -i T1image.nii.gz -s subject_name -all > > Below is error message on the screen: > #@# Smooth1 lh Mon Aug 20 23:51:55 EDT 2018 > /Volumes/AERS_BACKUP/Data/OSA/FREESURFER/OSA_048/scripts > \n mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix > ../surf/lh.smoothwm.nofix \n > setting seed for random number generator to 1234 > mris_smooth(27701,0x7fffec01b3c0) malloc: *** > mach_vm_map(size=13835344293369151488) failed (error code=3) > *** error: can't allocate region > *** set a breakpoint in malloc_error_break to debug > TAGskip: tag=-8454144, failed to calloc 4286513152 bytes! > > Cannot allocate memory > Darwin lspfis-imac.uphs.upenn.edu <http://lspfis-imac.uphs.upenn.edu%3E
> 16.7.0 Darwin Kernel Version 16.7.0: Fri Apr 27 17:59:46 PDT2018;
> root:xnu-3789.73.13~1/RELEASE_X86_64 x86_64 > > recon-all -s OSA_048 exited with ERRORS at Mon Aug 20 23:51:55EDT 2018
> Although the message looks like the shortage of memory, it couldrun a
> few weeks ago. So, I really doubt memory is the main reason (the > physical memory is 40GB)...The only difference before and afterI can
> run is I reinstall the same version of Matlab 2016b by accident.Do
> you think I have to change some setting to run it? > > Also, I've looked for solutions and couldn't find a one whichreally
> fits my problem. Would you please help me trouble-shoot thisissue?
> Thank you so much. > > 1) FreeSurferversion: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
> 2) Platform: macOS Sierra version 10.12.6, with physical memory40GB
> 3) uname -a: Darwin lspfis-imac.uphs.upenn.edu > <http://lspfis-imac.uphs.upenn.edu> 16.7.0 Darwin Kernel Version > 16.7.0: Fri Apr 27 17:59:46 PDT 2018; > root:xnu-3789.73.13~1/RELEASE_X86_64 x86_64 > 4) recon-all.log: see attached > > > Best, > > PH > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person towhom it is
addressed. If you believe this e-mail was sent to you in error andthe e-mail
contains patient information, please contact the PartnersCompliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sentto you in error
but does not contain patient information, please contact thesender and properly
dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
You mentioned things had worked fine a few weeks ago, but was that with the same subject? Can you run "tar -czf" on the subject directory and send the compressed file over via ftp? Instructions are at http://freesurfer.net/fswiki/FtpFileExchange thanks, Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Paysing Wu paysingwu@gmail.com Reply-To: FS Help freesurfer@nmr.mgh.harvard.edu Date: Wednesday, August 22, 2018 at 1:56 PM To: FS Help freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_smooth error: can't allocate region
External Email - Use Caution Hi Bruce,
This is the FS version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c I reinstalled the MATLAB. Do you think this will result in the issue?
Thanks,
PH
On Wed, Aug 22, 2018 at 4:12 PM Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote: what version of FS are you using? I think this is a bug that we had years ago for only a few weeks. One workaround would be to load each .mgz volume into matlab and write them back out (which will strip all the tags from them). I'm not sure why you are having the problem though Bruce
On Wed, 22 Aug 2018, Paysing Wu wrote:
External Email - Use CautionHi Douglas, Yes, I did try similar way to see if it worked. I deleted the whole folder and re-ran it. It stoped at the same place. Is there any other suggestion I could try?
Thanks,
PH
On Wed, Aug 22, 2018 at 1:23 PM Douglas N. Greve <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu> wrote: It looks like a corrupted file. Try renaming/deleting lh.orig.nofix, regenerating it, then seeing if mris_smooth works.
On 08/22/2018 10:44 AM, Paysing Wu wrote: > > External Email - Use Caution > > Hi FreeSurfer Developers, > > I was running recon-all and it stoped at smooth1. The command is: > recon-all -i T1image.nii.gz -s subject_name -all > > Below is error message on the screen: > #@# Smooth1 lh Mon Aug 20 23:51:55 EDT 2018 > /Volumes/AERS_BACKUP/Data/OSA/FREESURFER/OSA_048/scripts > \n mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix > ../surf/lh.smoothwm.nofix \n > setting seed for random number generator to 1234 > mris_smooth(27701,0x7fffec01b3c0) malloc: *** > mach_vm_map(size=13835344293369151488) failed (error code=3) > *** error: can't allocate region > *** set a breakpoint in malloc_error_break to debug > TAGskip: tag=-8454144, failed to calloc 4286513152 bytes! > > Cannot allocate memory > Darwin lspfis-imac.uphs.upenn.edu<http://lspfis-imac.uphs.upenn.edu> <http://lspfis-imac.uphs.upenn.edu> > 16.7.0 Darwin Kernel Version 16.7.0: Fri Apr 27 17:59:46 PDT 2018; > root:xnu-3789.73.13~1/RELEASE_X86_64 x86_64 > > recon-all -s OSA_048 exited with ERRORS at Mon Aug 20 23:51:55 EDT 2018 > Although the message looks like the shortage of memory, it could run a > few weeks ago. So, I really doubt memory is the main reason (the > physical memory is 40GB)...The only difference before and after I can > run is I reinstall the same version of Matlab 2016b by accident. Do > you think I have to change some setting to run it? > > Also, I've looked for solutions and couldn't find a one which really > fits my problem. Would you please help me trouble-shoot this issue? > Thank you so much. > > 1) FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c > 2) Platform: macOS Sierra version 10.12.6, with physical memory 40GB > 3) uname -a: Darwin lspfis-imac.uphs.upenn.edu<http://lspfis-imac.uphs.upenn.edu> > <http://lspfis-imac.uphs.upenn.edu> 16.7.0 Darwin Kernel Version > 16.7.0: Fri Apr 27 17:59:46 PDT 2018; > root:xnu-3789.73.13~1/RELEASE_X86_64 x86_64 > 4) recon-all.log: see attached > > > Best, > > PH > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Douglas N. Greve -
Hoopes, Andrew -
Paysing Wu