Hi free surfer users and developers,
for the first time I got this error after running recon-all:
CORRECTING DEFECT 76 (vertices=36299, convex hull=8085) mris_fix_topology(74305) malloc: *** mmap(size=1148719104) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Bus error Darwin HG-01881507-DM7.local 11.4.0 Darwin Kernel Version 11.4.0: Mon Apr 9 19:32:15 PDT 2012; root:xnu-1699.26.8~1/RELEASE_X86_64 x86_64
recon-all -s 122 exited with ERRORS at Sat Oct 13 22:31:01 EDT 2012
What can I do to fix the problem?
Thanks in advance,
Pietro
Hi Pietro
that's a pretty big defect. Have you checked the ?h.orig.nofix to see why it is so large? The other problem is that the current FS mac release is 32 bit, which is why you are running out of memory. It would work properly on a Linux box with more ram I suspect. We are hoping to have a 64 bit mac release soon, but in the interim I would suggest you track down the cause of your huge defect and correct it either with control points, or by editing the wm.mgz
cheers Bruce
On Mon, 15 Oct 2012, pietro de rossi wrote:
Hi free surfer users and developers, for the first time I got this error after running recon-all:
CORRECTING DEFECT 76 (vertices=36299, convex hull=8085) mris_fix_topology(74305) malloc: *** mmap(size=1148719104) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Bus error Darwin HG-01881507-DM7.local 11.4.0 Darwin Kernel Version 11.4.0: Mon Apr 9 19:32:15 PDT 2012; root:xnu-1699.26.8~1/RELEASE_X86_64 x86_64
recon-all -s 122 exited with ERRORS at Sat Oct 13 22:31:01 EDT 2012
What can I do to fix the problem?
Thanks in advance,
Pietro
-- Pietro De Rossi, MD
Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma
NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant?Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy
Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
Thanks Bruce.
is it possible that this is a problem of the scan I was running? The other 5 scans I was running in parallel went through without errors... I'm checking control points and wm.mgz anyway...
2012/10/15 Bruce Fischl fischl@nmr.mgh.harvard.edu
Hi Pietro
that's a pretty big defect. Have you checked the ?h.orig.nofix to see why it is so large? The other problem is that the current FS mac release is 32 bit, which is why you are running out of memory. It would work properly on a Linux box with more ram I suspect. We are hoping to have a 64 bit mac release soon, but in the interim I would suggest you track down the cause of your huge defect and correct it either with control points, or by editing the wm.mgz
cheers Bruce
On Mon, 15 Oct 2012, pietro de rossi wrote:
Hi free surfer users and developers,
for the first time I got this error after running recon-all:
CORRECTING DEFECT 76 (vertices=36299, convex hull=8085) mris_fix_topology(74305) malloc: *** mmap(size=1148719104) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Bus error Darwin HG-01881507-DM7.local 11.4.0 Darwin Kernel Version 11.4.0: Mon Apr 9 19:32:15 PDT 2012; root:xnu-1699.26.8~1/RELEASE_**X86_64 x86_64
recon-all -s 122 exited with ERRORS at Sat Oct 13 22:31:01 EDT 2012
What can I do to fix the problem?
Thanks in advance,
Pietro
-- Pietro De Rossi, MD ------------------------------**------- Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma
NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant?Andrea Hospital,
Via di Grottarossa 1035-1039, 00189 Rome, Italy
Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
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/**compliancelinehttp://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.
Hi Pietro,
yes, possibly. Subject motion can cause this to happen.
cheers Bruce On Mon, 15 Oct 2012, pietro de rossi wrote:
Thanks Bruce. is it possible that this is a problem of the scan I was running? The other 5 scans I was running in parallel went through without errors... I'm checking control points and wm.mgz anyway...
2012/10/15 Bruce Fischl fischl@nmr.mgh.harvard.edu Hi Pietro
that's a pretty big defect. Have you checked the ?h.orig.nofix to see why it is so large? The other problem is that the current FS mac release is 32 bit, which is why you are running out of memory. It would work properly on a Linux box with more ram I suspect. We are hoping to have a 64 bit mac release soon, but in the interim I would suggest you track down the cause of your huge defect and correct it either with control points, or by editing the wm.mgz cheers Bruce On Mon, 15 Oct 2012, pietro de rossi wrote: Hi free surfer users and developers, for the first time I got this error after running recon-all: CORRECTING DEFECT 76 (vertices=36299, convex hull=8085) mris_fix_topology(74305) malloc: *** mmap(size=1148719104) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Bus error Darwin HG-01881507-DM7.local 11.4.0 Darwin Kernel Version 11.4.0: Mon Apr 9 19:32:15 PDT 2012; root:xnu-1699.26.8~1/RELEASE_X86_64 x86_64 recon-all -s 122 exited with ERRORS at Sat Oct 13 22:31:01 EDT 2012 What can I do to fix the problem? Thanks in advance, Pietro -- Pietro De Rossi, MD ------------------------------------- Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions),School of Medicine and Psychology, Sapienza University, Sant?Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy
Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
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.
-- Pietro De Rossi, MD
Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma
NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant?Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy
Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
you were right Bruce, motion artefacts are VERY bad in that scan. I don't think I can even edit it properly.
Talking about editing however, I posted something last week but no-one replied, I'm afraid the email was blocked due to attachment issues.
It was about control points and topological defects in temporal lobe.
should I repost the email?
Sorry for bothering,
Pietro
2012/10/15 Bruce Fischl fischl@nmr.mgh.harvard.edu
Hi Pietro,
yes, possibly. Subject motion can cause this to happen.
cheers Bruce On Mon, 15 Oct 2012, pietro de rossi wrote:
Thanks Bruce.
is it possible that this is a problem of the scan I was running? The other 5 scans I was running in parallel went through without errors... I'm checking control points and wm.mgz anyway...
2012/10/15 Bruce Fischl fischl@nmr.mgh.harvard.edu Hi Pietro
that's a pretty big defect. Have you checked the ?h.orig.nofix to see why it is so large? The other problem is that the current FS mac release is 32 bit, which is why you are running out of memory. It would work properly on a Linux box with more ram I suspect. We are hoping to have a 64 bit mac release soon, but in the interim I would suggest you track down the cause of your huge defect and correct it either with control points, or by editing the wm.mgz cheers Bruce On Mon, 15 Oct 2012, pietro de rossi wrote: Hi free surfer users and developers, for the first time I got this error after running recon-all: CORRECTING DEFECT 76 (vertices=36299, convex hull=8085) mris_fix_topology(74305) malloc: *** mmap(size=1148719104) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Bus error Darwin HG-01881507-DM7.local 11.4.0 Darwin Kernel Version 11.4.0: Mon Apr 9 19:32:15 PDT 2012; root:xnu-1699.26.8~1/RELEASE_**X86_64 x86_64 recon-all -s 122 exited with ERRORS at Sat Oct 13 22:31:01 EDT 2012 What can I do to fix the problem? Thanks in advance, Pietro -- Pietro De Rossi, MD ------------------------------**------- Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions),School of Medicine and Psychology, Sapienza University, Sant?Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy
Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
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/**compliancelinehttp://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.
-- Pietro De Rossi, MD ------------------------------**------- Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma
NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant?Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy
Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
pietro de rossi