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> 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> 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
> 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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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.