Hi all,<br><br>Since upgrading to Freesurfer v5.0, I have been unable to complete the first step of recon-all (&#39;recon-all -autorecon1 -subjid ...&#39;) 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:<br>
=========================<br>Resolution: 0<br> Iteration(single-prec): 1 (subsample 200) mri_robust_template(47536) malloc: *** mmap(size=921600) failed (error code=12)<br>*** error: can&#39;t allocate region<br>*** set a breakpoint in malloc_error_break to debug<br>
MRIalloc(480, 480, 248): could not allocate 921600 bytes for 207th slice<br><br>Cannot allocate memory<br>/Users/mahen/fMRI/Surfaces/cck_kmu<br>\n mri_convert /Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz /Users/mahen/fMRI/Surfaces/cck_kmu/mri/orig.mgz --conform \n<br>
mri_convert /Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz /Users/mahen/fMRI/Surfaces/cck_kmu/mri/orig.mgz --conform <br>mghRead(/Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz, -1): could not open file<br>$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $<br>
reading from /Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz...<br>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<br><br>recon-all -s cck_kmu exited with ERRORS at Tue Feb  8 20:50:00 CST 2011<br>
=====================<br>My machine has 4gb of RAM, and I&#39;ve ssh&#39;d into my advisor&#39;s machine (which has 16gb) and had the same problem.<br>I tryed updating the binaries for recon-all and mri_robust_template (from <a href="http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-leopard-intel/">http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-leopard-intel/</a>), but the problem remained unsolved.<br>
My advisor informs me that it is now running with version 4.5 (all 5 anatomicals); I&#39;d still like to know what&#39;s going on. I have tried running it on version 5 with just 2 anatomical datasets, and it works just fine.<br>
<br>Here is the output of bugr:<br><br>FREESURFER_HOME: /Applications/freesurfer<br><br>Build stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0<br><br>Kernel info: Darwin 10.6.0 i386<br><br>Thanks in advance,<br>Mahen<br>