Hello,
I am having a problem with mri_robust_template using too much RAM and
causing my computers to freeze. I am using fs510. I think I would like to
try to convert the inputs to uchar as Martin suggested, but I am not sure
exactly where to do this. Would I issue this command:
For each timepoint:
mv tp1/mri/norm.mgz tp1/mri/norm.orig.mgz
mri_convert -i tp1/mri/norm.orig.mgz -o tp1/mri/norm/mgz -odt uchar
recon-all -base -tp 1 -tp 2 -all
Also, my computers have two AMD processors and 4GB of DDR RAM running at
333MHZ. I dropped them down so they each only do one job, but they are
still freezing. Besides upgrading the entire cluster to something more
current, would doubling the RAM to 8GB be worthwhile?
As always, thank you so very much!
Jeff Sadino
Mahen
Fri, 11 Feb 2011 09:16:27 -0800
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
<mreu...@nmr.mgh.harvard.edu>wrote:
> 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-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
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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