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: [email protected]
> phone: 734-615-5155
>
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