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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