Hi all,
Since upgrading to Freesurfer v5.0, I have been unable to complete the first
step of recon-all ('recon-all -autorecon1 -subjid ...') when using 5
anatomical datasets (our typical load for surface reconstruction). The
problem seems to come when the third dataset is being registered, at which
point recon-all exits with the following error message:
=========================
Resolution: 0
Iteration(single-prec): 1 (subsample 200) mri_robust_template(47536)
malloc: *** mmap(size=921600) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
MRIalloc(480, 480, 248): could not allocate 921600 bytes for 207th slice
Cannot allocate memory
/Users/mahen/fMRI/Surfaces/cck_kmu
\n mri_convert /Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz
/Users/mahen/fMRI/Surfaces/cck_kmu/mri/orig.mgz --conform \n
mri_convert /Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz
/Users/mahen/fMRI/Surfaces/cck_kmu/mri/orig.mgz --conform
mghRead(/Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz, -1): could not
open file
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from /Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz...
Darwin MahenWillEatYourChildren.local 10.6.0 Darwin Kernel Version 10.6.0:
Wed Nov 10 18:13:17 PST 2010; root:xnu-1504.9.26~3/RELEASE_I386 i386
recon-all -s cck_kmu exited with ERRORS at Tue Feb 8 20:50:00 CST 2011
=====================
My machine has 4gb of RAM, and I've ssh'd into my advisor's machine (which
has 16gb) and had the same problem.
I tryed updating the binaries for recon-all and mri_robust_template (from
http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-leopard-intel/),
but the problem remained unsolved.
My advisor informs me that it is now running with version 4.5 (all 5
anatomicals); I'd still like to know what's going on. I have tried running
it on version 5 with just 2 anatomical datasets, and it works just fine.
Here is the output of bugr:
FREESURFER_HOME: /Applications/freesurfer
Build stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0
Kernel info: Darwin 10.6.0 i386
Thanks in advance,
Mahen
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