Re: [Freesurfer] malloc_error_break/ can't allocate region

2016-08-17 Thread zkaufman 
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, miracoo...@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
>>> <gr...@nmr.mgh.harvard.edu <mailto:gr...@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 1 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 1"
>>>>
>>>> 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
>>> gr...@nmr.mgh.harvard.edu <mailto: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: 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 pati

Re: [Freesurfer] malloc_error_break/ can't allocate region

2016-08-17 Thread Douglas N Greve 
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, miracoo...@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
>> <gr...@nmr.mgh.harvard.edu <mailto:gr...@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 1 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 1"
>>>
>>> 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
>> gr...@nmr.mgh.harvard.edu <mailto: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: 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.
>>
>>
>>
>>
>> ___
>> 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
gr...@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/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] malloc_error_break/ can't allocate region

2016-08-17 Thread miracooloz 
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 
> <gr...@nmr.mgh.harvard.edu <mailto:gr...@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 1 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 1"
> >
> > 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
> gr...@nmr.mgh.harvard.edu <mailto: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: 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.
>
>
>
>
> ___
> 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
gr...@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/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] malloc_error_break/ can't allocate region

2016-08-16 Thread miracle ozzoude 
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 
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 1 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 1"
> >
> > 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
> gr...@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/
>
> ___
> 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.
>
>
___
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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 . 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.

Re: [Freesurfer] malloc_error_break/ can't allocate region

2016-08-16 Thread Douglas N Greve 
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 1 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 1"
>
> 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
gr...@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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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.