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-int...), 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
Hi Mahen,
4.5 is based on flirt registration which does a pairwise registration to the first image. Since 5.0 we use the mri_robust_template tool (as it can ignore outlier regions and produces more accurate registrations, see Reuter et al Neuroimage 2010 "..robust registration"), but it is more memory hungry and time consuming.
If your input images are large, it can happen that mri_robust_template uses a lot of memory. I tested that tool in the longitudinal stream where I successfully ran it on > 10 images on a 4 gig machine (those images are probably smaller than yours).
So you have the following options:
1. use only the best 2 input images. This has been recommended in the past, 5 inputs are usually not improving anything (see old emails on this list from Bruce)
2. pass the flag -flirt-motioncor to recon-all and it will revert back to using flirt (but accuracy of the registration might suffer, since the inputs are full head images with potentially a lot of differences in jaw, tongue, neck, eyes, scalp and cropping planes).
Another option would be to convert the inputs to uchar and see if that fits into the memory. They will be converted to uchar anyway in the conform step.
Best, Martin
On Tue, 2011-02-08 at 23:21 +0800, Mahen wrote:
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-int...), 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
To Martin,
Thanks a bunch. I haven't tested out all the recommendations, but at least I know what's going on. If I did want to convert to uchar, how would I go about this? Is there a function included in the Freesurfer package, or would I have to write my own function to do so? It's not a concern, as I'm probably not going to explore this avenue, but if I get time, I might enjoy trying to write such a function...
Regards, Mahen
On Wed, Feb 9, 2011 at 7:07 AM, Martin Reuter mreuter@nmr.mgh.harvard.eduwrote:
Hi Mahen,
4.5 is based on flirt registration which does a pairwise registration to the first image. Since 5.0 we use the mri_robust_template tool (as it can ignore outlier regions and produces more accurate registrations, see Reuter et al Neuroimage 2010 "..robust registration"), but it is more memory hungry and time consuming.
If your input images are large, it can happen that mri_robust_template uses a lot of memory. I tested that tool in the longitudinal stream where I successfully ran it on > 10 images on a 4 gig machine (those images are probably smaller than yours).
So you have the following options:
- use only the best 2 input images. This has been recommended in the
past, 5 inputs are usually not improving anything (see old emails on this list from Bruce)
- pass the flag -flirt-motioncor to recon-all and it will revert back
to using flirt (but accuracy of the registration might suffer, since the inputs are full head images with potentially a lot of differences in jaw, tongue, neck, eyes, scalp and cropping planes).
Another option would be to convert the inputs to uchar and see if that fits into the memory. They will be converted to uchar anyway in the conform step.
Best, Martin
On Tue, 2011-02-08 at 23:21 +0800, Mahen wrote:
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-int...), 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Mahen -
Martin Reuter