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
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
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/
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.
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> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: 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/ _______________________________________________ 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.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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/
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.
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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.
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> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: 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/ _______________________________________________ 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.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.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
That fixed the error.
Thank you so much for your help!
Marissa Pifer
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 onthe
> 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> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: 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/ _______________________________________________ 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.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.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/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas Greve -
Douglas N Greve
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Marissa Pifer