Hi Vincent,
On May 7, 2013, at 23:20 , Vincent Koppelmans wrote:
Dear FreeSurfer experts,
I am trying to create a template for a longitudinal analysis. For each subject I have 7 time points. The resolution of the T1 images is 1.0x0.98x0.98 mm.
The first step (i.e. the cross-sectional processing) finished without errors for all participants for all time points.
The second step (i.e. the template creation) stopped while processing the third time point (see attached log file).
My Machine is running OSX 10.8.3, with FreeSurfer version 5.1.0. I have 16 gb of memory installed. During the run FS was using up only 3gb and there was still 6gb available.
If I recall correctly, 5.1 was only distributed as 32bit binaries, so FS will only be able to address at max 4GB (and more likely only 3GB due to reserve 1GB of address space for the kernel, but I do not recall the details for Macosx). You can test that hypothesis by running the following in a terminal (after sourcing for free surfer environment):
file `which mri_average`
if you get something like: /opt/freesurfer-Darwin-lion-stable-pub-v5.2.0/bin/mri_average: Mach-O 64-bit executable x86_64 you have a 64bit built (as indicated by executable x86_64), if you get something similar to: /opt/freesurfer/bin/mri_average: Mach-O executable i386 you are stuck at 32bit. I guess the best solution would be to wait for the bug fixed free surfer 5.3 (which should be around soon) and then redo your analyses, hopping that the additional 6GB will allow your analyses to finish.
best regards Sebastian
How can I solve this problem?
Thanks,
Vincent
LOG FILE:
Tue May 7 13:58:41 EDT 2013 /Volumes/Data/tmp/Bedrest/FreeSurfer/8936 /Applications/freesurfer/bin/recon-all -base 8936 -tp 8936_01 -tp 8936_02 -tp 8936_03 -tp 8936_04 -tp 8936_05 -tp 8936_06 -tp 8936_07 -all subjid 8936 setenv SUBJECTS_DIR /Volumes/Data/tmp/Bedrest/FreeSurfer FREESURFER_HOME /Applications/freesurfer Actual FREESURFER_HOME /Applications/freesurfer build-stamp.txt: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Darwin x.kines.umich.edu 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 256 memorylocked unlimited maxproc 709
PhysMem: 1733M wired, 4205M active, 1281M inactive, 7219M used, 9155M free.
(here some stuff happens which I have left out)
Finished TP : 2
=====================================================
Working on TP 3
Registration::computeMultiresRegistration
- Gaussian Pyramid
- Gaussian Pyramid
- initial transform:
Ti = [ ... 0.9996153712273 0.0026029755827 -0.0276110433042 0.1370086669922 -0.0021083820611 0.9998371005058 0.0179268959910 9.5177154541016 0.0276532080024 -0.0178617853671 0.9994579553604 10.5185699462891 0 0 0 1.0000000000000 ]
- initial iscale: Ii =1
Resolution: 4 S( 16 16 16 ) T( 16 16 16 ) Iteration(f): 1 -- diff. to prev. transform: 1.73616 Iteration(f): 2 -- diff. to prev. transform: 0.231302 Iteration(f): 3 -- diff. to prev. transform: 0.247707 Iteration(f): 4 -- diff. to prev. transform: 0.0780292 Iteration(f): 5 -- diff. to prev. transform: 0.0629118 max it: 5 reached!
Resolution: 3 S( 32 32 32 ) T( 32 32 32 ) Iteration(f): 1 -- diff. to prev. transform: 1.54023 Iteration(f): 2 -- diff. to prev. transform: 0.389993 Iteration(f): 3 -- diff. to prev. transform: 0.121733 Iteration(f): 4 -- diff. to prev. transform: 0.180449 Iteration(f): 5 -- diff. to prev. transform: 0.0662501 max it: 5 reached!
Resolution: 2 S( 64 64 64 ) T( 64 64 64 ) Iteration(f): 1 -- diff. to prev. transform: 0.749486 Iteration(f): 2 -- diff. to prev. transform: 0.0109516 Iteration(f): 3 -- diff. to prev. transform: 0.00196896 < 0.01 :-)
Resolution: 1 S( 128 128 128 ) T( 128 128 128 ) Iteration(f): 1 -- diff. to prev. transform: 0.421039 Iteration(f): 2 -- diff. to prev. transform: 0.00943852 < 0.01 :-)
Resolution: 0 S( 256 256 256 ) T( 256 256 256 ) Iteration(f): 1 -- diff. to prev. transform: 0.102893 Iteration(f): 2mri_robust_template(40563) malloc: *** mmap(size=262144) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(256, 256, 256): could not allocate 262144 bytes for 228th slice
Cannot allocate memory Darwin x.kines.umich.edu 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64
recon-all -s 8936 exited with ERRORS at Tue May 7 14:23:40 EDT 2013
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Vincent Koppelmans, PhD University of Michigan School of Kinesiology Neuromotor Behavior Lab 401 Washtenaw Ave. Ann Arbor, MI 48109-2214 email: vkoppel@umich.edu phone: 734-615-5155
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