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.
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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