Freesurfer users,
I have ran into a malloc error running trac-all. Looks like the same error that Stijn posted to the list on 17 Jun 2011. I did not see a solution posted. It occurs in dmr_train using trac-all -prep –c dmrirc.txt. Also tried using trac-all –prior –c dmrirc.txt with the same results. Reset the tcsh limits for datasize, ….
********* Loading segmentation from /Applications/freesurfer5_1/trctrain/trc029/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /Applications/freesurfer5_1/trctrain/trc029/dlabel/mni/cortex+2mm.nii.gz dmri_train(54615) malloc: *** mmap(size=159744) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(218, 182, 182): could not allocate 158704 bytes for 26th slice
Cannot allocate memory ********** My system
Model Name: Mac Pro
Model Identifier: MacPro3,1
Processor Name: Quad-Core Intel Xeon
Processor Speed: 2.8 GHz
Number Of Processors: 2
Total Number Of Cores: 8
L2 Cache (per processor): 12 MB
Memory: 18 GB
System Version: Mac OS X 10.5.8
Thanks for any advice or suggestions!
Kevin Dabbs
SMPH/Neurology UW-Madison
Hi Kevin - This is unfortunately a problem with the macos freesurfer distribution, which is still built on leopard instead of snow leopard b/c of compatibility issues with some libraries unrelated to tracula. It's possible to compile tracula on snow leopard (in fact that's what I use) but you'd have to download the source code.
Since several people have written about this by now, I'm considering something that'd be less of a pain for users, which is to create a tarball with only the tracula executables compiled on snow leopard and make it available.
a.y
On Fri, 22 Jul 2011, Dabbs (Kevin) wrote:
Freesurfer users,
I have ran into a malloc error running trac-all. Looks like the same error that Stijn posted to the list on 17 Jun 2011. I did not see a solution posted. It occurs in dmr_train using trac-all -prep –c dmrirc.txt. Also tried using trac-all –prior –c dmrirc.txt with the same results. Reset the tcsh limits for datasize, ….
Loading segmentation from /Applications/freesurfer5_1/trctrain/trc029/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /Applications/freesurfer5_1/trctrain/trc029/dlabel/mni/cortex+2mm.nii.gz dmri_train(54615) malloc: *** mmap(size=159744) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(218, 182, 182): could not allocate 158704 bytes for 26th slice
Cannot allocate memory
My system
Model Name: Mac Pro
Model Identifier: MacPro3,1
Processor Name: Quad-Core Intel Xeon
Processor Speed: 2.8 GHz
Number Of Processors: 2
Total Number Of Cores: 8
L2 Cache (per processor): 12 MB
Memory: 18 GB
System Version: Mac OS X 10.5.8
Thanks for any advice or suggestions!
Kevin Dabbs
SMPH/Neurology UW-Madison
Hi Anastasia,
Having the same issue, I was wondering if it's possible to recompile only tracula from the source code ? If yes could you give some hints ?
Thanks a lot, Dr. David Coynel Division of Cognitive Neuroscience University of Basel Birmannsgasse 8 4055 Basel - Switzerland david.coynel@unibas.ch tel: +41(0)612.670.240
Am 22.07.2011 um 16:36 schrieb Anastasia Yendiki:
Hi Kevin - This is unfortunately a problem with the macos freesurfer distribution, which is still built on leopard instead of snow leopard b/c of compatibility issues with some libraries unrelated to tracula. It's possible to compile tracula on snow leopard (in fact that's what I use) but you'd have to download the source code.
Since several people have written about this by now, I'm considering something that'd be less of a pain for users, which is to create a tarball with only the tracula executables compiled on snow leopard and make it available.
a.y
On Fri, 22 Jul 2011, Dabbs (Kevin) wrote:
Freesurfer users, I have ran into a malloc error running trac-all. Looks like the same error that Stijn posted to the list on 17 Jun 2011. I did not see a solution posted. It occurs in dmr_train using trac-all -prep –c dmrirc.txt. Also tried using trac-all –prior –c dmrirc.txt with the same results. Reset the tcsh limits for datasize, ….
Loading segmentation from /Applications/freesurfer5_1/trctrain/trc029/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /Applications/freesurfer5_1/trctrain/trc029/dlabel/mni/cortex+2mm.nii.gz dmri_train(54615) malloc: *** mmap(size=159744) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(218, 182, 182): could not allocate 158704 bytes for 26th slice Cannot allocate memory
My system Model Name: Mac Pro Model Identifier: MacPro3,1 Processor Name: Quad-Core Intel Xeon Processor Speed: 2.8 GHz Number Of Processors: 2 Total Number Of Cores: 8 L2 Cache (per processor): 12 MB Memory: 18 GB System Version: Mac OS X 10.5.8 Thanks for any advice or suggestions! Kevin Dabbs SMPH/Neurology UW-Madison
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Anastasia Yendiki -
Dabbs (Kevin) -
David Coynel