On Wed, May 11, 2016 at 11:32 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

Try re-running recon-all -qcache for that subject and see if the error
goes away

On 05/11/2016 10:56 AM, Marissa Pifer wrote:
> The error was generated on that first subject 03-1, but it was
> successful on all of the other subjects. Is there something wrong with
> that file that we have to exclude that subject from the analysis?
>
> Marissa
>
> On Wed, May 11, 2016 at 10:38 AM, Douglas Greve

> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
> OK, it is failing on the mri_concat command. It may be that one
> of those inputs is causing the problem. Can you run the command
> with each input separately, eg,
> mri_concat
> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR03-1.long.SOAR03/surf/lh.thickness.fwhm10.fsaverage.mgh
> --o deleteme.mgh
> mri_concat
> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR03-2.long.SOAR03/surf/lh.thickness.fwhm10.fsaverage.mgh
> --o deleteme.mgh
> ...
>
> and see if there is one that generates the error
>
>
>
> On 5/11/16 9:15 AM, Marissa Pifer wrote:
>> Here is everything in the terminal after I hit analyze:
>>
>> Data table loading completed successfully.
>>
>> SUBJECTS_DIR is '/Users/marchaut/Documents/myprojects/SOARmaster'
>>
>> lh-Avg-Intercept-thickness -----------------------
>>
>> Does the average thickness differ from zero?
>>
>> 1.000 1.000;
>>
>>
>> lh-Diff-1-2-Intercept-thickness -----------------------
>>
>> Does the average thickness differ between 1 and 2?
>>
>> 1.000 -1.000;
>>
>>
>> ninputs = 28
>>
>> Checking inputs
>>
>> mri_concat(4256,0x7fff78a00310) malloc: ***
>> mach_vm_map(size=4619122851646017536) failed (error code=3)
>>
>> *** error: can't allocate region
>>
>> *** set a breakpoint in malloc_error_break to debug
>>
>> znzTAGskip: tag=586130367, failed to calloc 2856323072 bytes!
>>
>>
>> Cannot allocate memory
>>
>> Error in Analyze: command failed: mri_concat
>> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR03-1.long.SOAR03/surf/lh.thickness.fwhm10.fsaverage.mgh
>> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR03-2.long.SOAR03/surf/lh.thickness.fwhm10.fsaverage.mgh
>> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR04-1.long.SOAR04/surf/lh.thickness.fwhm10.fsaverage.mgh
>> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR04-2.long.SOAR04/surf/lh.thickness.fwhm10.fsaverage.mgh
>> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR05-1.long.SOAR05/surf/lh.thickness.fwhm10.fsaverage.mgh
>> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR05-2.long.SOAR05/surf/lh.thickness.fwhm10.fsaverage.mgh
>> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR06-1.long.SOAR06/surf/lh.thickness.fwhm10.fsaverage.mgh
>> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR06-2.long.SOAR06/surf/lh.thickness.fwhm10.fsaverage.mgh
>> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR07-1.long.SOAR07/surf/lh.thickness.fwhm10.fsaverage.mgh
>> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR07-2.long.SOAR07/surf/lh.thickness.fwhm10.fsaverage.mgh
>> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR09-1.long.SOAR09/surf/lh.thickness.fwhm10.fsaverage.mgh
>> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR09-2.long.SOAR09/surf/lh.thickness.fwhm10.fsaverage.mgh
>> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR17-1.long.SOAR17/surf/lh.thickness.fwhm10.fsaverage.mgh
>> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR17-2.long.SOAR17/surf/lh.thickness.fwhm10.fsaverage.mgh
>> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR19-1.long.SOAR19/surf/lh.thickness.fwhm10.fsaverage.mgh
>> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR19-2.long.SOAR19/surf/lh.thickness.fwhm10.fsaverage.mgh
>> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR23-1.long.SOAR23/surf/lh.thickness.fwhm10.fsaverage.mgh
>> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR23-2.long.SOAR23/surf/lh.thickness.fwhm10.fsaverage.mgh
>> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR26-1.long.SOAR26/surf/lh.thickness.fwhm10.fsaverage.mgh
>> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR26-2.long.SOAR26/surf/lh.thickness.fwhm10.fsaverage.mgh
>> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR27-1.long.SOAR27/surf/lh.thickness.fwhm10.fsaverage.mgh
>> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR27-2.long.SOAR27/surf/lh.thickness.fwhm10.fsaverage.mgh
>> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR28-1.long.SOAR28/surf/lh.thickness.fwhm10.fsaverage.mgh
>> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR28-2.long.SOAR28/surf/lh.thickness.fwhm10.fsaverage.mgh
>> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR30-1.long.SOAR30/surf/lh.thickness.fwhm10.fsaverage.mgh
>> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR30-2.long.SOAR30/surf/lh.thickness.fwhm10.fsaverage.mgh
>> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR31-1.long.SOAR31/surf/lh.thickness.fwhm10.fsaverage.mgh
>> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR31-2.long.SOAR31/surf/lh.thickness.fwhm10.fsaverage.mgh
>> --o /Users/marchaut/Documents/myprojects/SOARmaster/qdec/test1/y.mgh
>>
>> XIO: fatal IO error 35 (Resource temporarily unavailable) on X
>> server "/tmp/launch-NzfFao/org.macosforge.xquartz:0"
>>
>> after 16398 requests (16398 known processed) with 0 events
>> remaining.
>>
>>
>> On Tue, May 10, 2016 at 5:41 PM, Douglas N Greve

>> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>>
>> Is that all it says? At one point (about 3-4 years ago) we
>> would see
>> that error because some of our files got corrupted. Can you
>> send more of
>> the terminal output?
>>
>> On 05/10/2016 12:56 PM, Marissa Pifer wrote:
>> > Hi freesurfers,
>> >
>> > I am on a macbook pro OSX 10.9.5, trying to run an analysis
>> on qdec -
>> > freesurfer version 5.3. I am looking to analyze T2weighted
>> scans for
>> > 27 subjects through the qdec system. I keep getting this
>> error that it
>> > cannot allocate memory for the task. I'v been talking with
>> our IT
>> > people and they've told me I have more than enough space on the
>> > computer, so it must be an issue with the program or how
>> it's set up.
>> >
>> > This is the error message:
>> >
>> >
>> > *** error: can't allocate region
>> >
>> > *** set a breakpoint in malloc_error_break to debug
>> >
>> > znzTAGskip: tag=586130367, failed to calloc 2856323072 bytes!
>> >
>> >
>> > Cannot allocate memory
>> >
>> >
>> >
>> > Does anyone know what I can do to fix this problem?
>> >
>> > Thanks,
>> >
>> > Marissa
>> >
>> >
>> > _______________________________________________
>> > 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>
>>
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>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
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>>
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> The information in this e-mail is intended only for the person to
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--
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
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