Hello FreeSurfer team, While running monte carlo correction with 10000 reps (mri_mcsim) for the whole hemisphere, I received this error at 975 reps for the left hemisphere
" 975 3197.9 0 mri_mcsim(25495) malloc: ***mmap(size=16777216) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Bus error" What does this mean and how can I resolve it? Below was my mri_mcsim command line " mri_mcsim --o wholebrainanalysis/average/mult-comp-cor/fsaverage/lh/cortex --base mc-z --surface fsaverage lh --nreps 10000"
Thank you Paul
What version of FS (and mri_mcsim) are you using? Does it die if you run with just a few reps (eg, 100)?
On 08/16/2016 01:21 PM, miracle ozzoude wrote:
Hello FreeSurfer team, While running monte carlo correction with 10000 reps (mri_mcsim) for the whole hemisphere, I received this error at 975 reps for the left hemisphere
" 975 3197.9 0 mri_mcsim(25495) malloc: ***mmap(size=16777216) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Bus error" What does this mean and how can I resolve it? Below was my mri_mcsim command line " mri_mcsim --o wholebrainanalysis/average/mult-comp-cor/fsaverage/lh/cortex --base mc-z --surface fsaverage lh --nreps 10000"
Thank you Paul
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
FS 5.1.0. I tried it with 5000 reps for ROI analysis and it worked.
On Tue, Aug 16, 2016 at 3:46 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
What version of FS (and mri_mcsim) are you using? Does it die if you run with just a few reps (eg, 100)?
On 08/16/2016 01:21 PM, miracle ozzoude wrote:
Hello FreeSurfer team, While running monte carlo correction with 10000 reps (mri_mcsim) for the whole hemisphere, I received this error at 975 reps for the left hemisphere
" 975 3197.9 0 mri_mcsim(25495) malloc: ***mmap(size=16777216) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Bus error" What does this mean and how can I resolve it? Below was my mri_mcsim command line " mri_mcsim --o wholebrainanalysis/average/mult-comp-cor/fsaverage/lh/cortex --base mc-z --surface fsaverage lh --nreps 10000"
Thank you Paul
Freesurfer mailing list 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 Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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That sounds fishy. I would use the 5.3 or 6.0 version.
On 08/16/2016 03:51 PM, miracle ozzoude wrote:
FS 5.1.0. I tried it with 5000 reps for ROI analysis and it worked.
On Tue, Aug 16, 2016 at 3:46 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
What version of FS (and mri_mcsim) are you using? Does it die if you run with just a few reps (eg, 100)? On 08/16/2016 01:21 PM, miracle ozzoude wrote: > Hello FreeSurfer team, > While running monte carlo correction with 10000 reps (mri_mcsim) for > the whole hemisphere, I received this error at 975 reps for the left > hemisphere > > " 975 3197.9 0 mri_mcsim(25495) malloc: ***mmap(size=16777216) failed > (error code=12) > *** error: can't allocate region > *** set a breakpoint in malloc_error_break to debug > Bus error" > What does this mean and how can I resolve it? Below was my mri_mcsim > command line " mri_mcsim --o > wholebrainanalysis/average/mult-comp-cor/fsaverage/lh/cortex --base > mc-z --surface fsaverage lh --nreps 10000" > > Thank you > Paul > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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.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: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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.
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Sure. Also, do you know how I can upgrade to either without uninstalling FS 5.1?
Sent from my BlackBerry 10 smartphone. Original Message From: Douglas N Greve Sent: Tuesday, August 16, 2016 4:01 PM To: freesurfer@nmr.mgh.harvard.edu Reply To: Freesurfer support list Subject: Re: [Freesurfer] malloc_error_break/ can't allocate region
That sounds fishy. I would use the 5.3 or 6.0 version.
On 08/16/2016 03:51 PM, miracle ozzoude wrote:
FS 5.1.0. I tried it with 5000 reps for ROI analysis and it worked.
On Tue, Aug 16, 2016 at 3:46 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
What version of FS (and mri_mcsim) are you using? Does it die if you run with just a few reps (eg, 100)?
On 08/16/2016 01:21 PM, miracle ozzoude wrote:
Hello FreeSurfer team, While running monte carlo correction with 10000 reps (mri_mcsim) for the whole hemisphere, I received this error at 975 reps for the left hemisphere
" 975 3197.9 0 mri_mcsim(25495) malloc: ***mmap(size=16777216)
failed
(error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Bus error" What does this mean and how can I resolve it? Below was my mri_mcsim command line " mri_mcsim --o wholebrainanalysis/average/mult-comp-cor/fsaverage/lh/cortex --base mc-z --surface fsaverage lh --nreps 10000"
Thank you Paul
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
mailto: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.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: https://gate.nmr.mgh.harvard.edu/filedrop2 https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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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 sender and properly dispose of the e-mail.
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Zeke will know better than me, but I think the new version folder name will be different, so there should not be any conflict. You will just need to reference the new source file
On 08/17/2016 12:23 PM, miracooloz@gmail.com wrote:
Sure. Also, do you know how I can upgrade to either without uninstalling FS 5.1?
Sent from my BlackBerry 10 smartphone. Original Message From: Douglas N Greve Sent: Tuesday, August 16, 2016 4:01 PM To: freesurfer@nmr.mgh.harvard.edu Reply To: Freesurfer support list Subject: Re: [Freesurfer] malloc_error_break/ can't allocate region
That sounds fishy. I would use the 5.3 or 6.0 version.
On 08/16/2016 03:51 PM, miracle ozzoude wrote:
FS 5.1.0. I tried it with 5000 reps for ROI analysis and it worked.
On Tue, Aug 16, 2016 at 3:46 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
What version of FS (and mri_mcsim) are you using? Does it die if you run with just a few reps (eg, 100)?
On 08/16/2016 01:21 PM, miracle ozzoude wrote:
Hello FreeSurfer team, While running monte carlo correction with 10000 reps (mri_mcsim) for the whole hemisphere, I received this error at 975 reps for the left hemisphere
" 975 3197.9 0 mri_mcsim(25495) malloc: ***mmap(size=16777216)
failed
(error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Bus error" What does this mean and how can I resolve it? Below was my mri_mcsim command line " mri_mcsim --o wholebrainanalysis/average/mult-comp-cor/fsaverage/lh/cortex --base mc-z --surface fsaverage lh --nreps 10000"
Thank you Paul
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
mailto: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.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: https://gate.nmr.mgh.harvard.edu/filedrop2 https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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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 sender and properly dispose of the e-mail.
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Hello Paul,
Doug is essential correct. You can download 5.3 (or the development version) and just extract it to a different location. Something like:
$> mkdir /usr/local/freesurfer_5.3 $> tar -C /usr/local/freesurfer_5.3 -xzvf freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz
Then you are free to source either version - just make sure you to do in a separate terminal window. Also, You can download freesurfer 5.3 or the Development version (see "Development Version") from the following page:
https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
Hope this helps.
-Zeke
Zeke will know better than me, but I think the new version folder name will be different, so there should not be any conflict. You will just need to reference the new source file
On 08/17/2016 12:23 PM, miracooloz@gmail.com wrote:
Sure. Also, do you know how I can upgrade to either without uninstalling FS 5.1?
Sent from my BlackBerry 10 smartphone. Original Message From: Douglas N Greve Sent: Tuesday, August 16, 2016 4:01 PM To: freesurfer@nmr.mgh.harvard.edu Reply To: Freesurfer support list Subject: Re: [Freesurfer] malloc_error_break/ can't allocate region
That sounds fishy. I would use the 5.3 or 6.0 version.
On 08/16/2016 03:51 PM, miracle ozzoude wrote:
FS 5.1.0. I tried it with 5000 reps for ROI analysis and it worked.
On Tue, Aug 16, 2016 at 3:46 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
What version of FS (and mri_mcsim) are you using? Does it die if you run with just a few reps (eg, 100)?
On 08/16/2016 01:21 PM, miracle ozzoude wrote:
Hello FreeSurfer team, While running monte carlo correction with 10000 reps (mri_mcsim) for the whole hemisphere, I received this error at 975 reps for the left hemisphere
" 975 3197.9 0 mri_mcsim(25495) malloc: ***mmap(size=16777216)
failed
(error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Bus error" What does this mean and how can I resolve it? Below was my mri_mcsim command line " mri_mcsim --o wholebrainanalysis/average/mult-comp-cor/fsaverage/lh/cortex --base mc-z --surface fsaverage lh --nreps 10000"
Thank you Paul
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
mailto: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.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: https://gate.nmr.mgh.harvard.edu/filedrop2 https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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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 sender and properly dispose of the e-mail.
Freesurfer mailing list 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 Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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freesurfer@nmr.mgh.harvard.edu
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miracle ozzoude -
miracooloz＠gmail.com
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zkaufman＠nmr.mgh.harvard.edu