Hi Martin,

Thanks for your reply.

My iMac has 14 GB of RAM. However, the Mac OS version of FreeSurfer is only available as a 32-bit version, and thus any time FreeSurfer requires more than approximately 3.5 GB of memory it will exit with an error. Are there any plans yet for a 64-bit Mac OS version?

I have a number of clinical participants with between 3 and 8 scans (timepoints) that I wish to analyse longitudinally. I have already run the cross-sectional reconstructions, performed the necessary pial and white matter edits and inserted control points, and re-run all the cross sectional reconstructions again to take accounts of the edits.

If I cannot now create the template reconstructions in Mac OS with all of my timepoints for all of my participants, what are my options?

Is it possible to run the 64-bit Linux version of FreeSurfer using VirtualBox on my iMac?

Could I then just create the template reconstructions for all my participants using virtualbox linux and return to Mac OS to run the final longitudinal stream on all the participants? I am aware that there are differences in how the 64-bit linux and the 32-bit Mac OS FreeSurfers will approach the analysis, but if I confine my use of the 64-bit Linux to just the creation of the templates for both (clinical and control) groups, then any differences between the systems should not affect the between-group comparisons?

I do not have access to an actual Linux system.

Best regards,

EA Bowman

> From: mreuter@nmr.mgh.harvard.edu
> To: ea_bowman@hotmail.com
> Date: Mon, 30 Jul 2012 18:00:29 -0400
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] More than two time-points in longitudinal base = Memory allocation error?
>
> Hi Liz,
>
> you need more memory (see the error message: cannot allocate memory).
>
> Best, Martin
>
>
> On Mon, 2012-07-23 at 10:21 +1000, Liz Bowman wrote:
> > Hello,
> >
> >
> > I have several patients scans taken over multiple time points (up to
> > nine time points in some patients). I thought I might be able to use
> > these to create a base template for longitudinal processing, however
> > the process fails and exits with errors if I try to create a base with
> > more than two time points from a patient.
> >
> >
> > This is a sample of the error log of the most recent attempt, with
> > three timepoints:
> >
> >
> > Resolution: 1 S( 128 128 128 ) T( 128 128 128 )
> > Iteration(f): 1 -- diff. to prev. transform: 0.876663
> > Iteration(f): 2 -- diff. to prev. transform: 0.0148738
> > Iteration(f): 3 -- diff. to prev. transform: 0.00156813 < 0.01
> > :-)
> >
> >
> > Resolution: 0 S( 256 256 256 ) T( 256 256 256 )
> > Iteration(f): 1 -- diff. to prev. transform: 0.263086
> > Iteration(f): 2mri_robust_template(1035) malloc: ***
> > mmap(size=262144) failed (error code=12)
> > *** error: can't allocate region
> > *** set a breakpoint in malloc_error_break to debug
> > MRIalloc(256, 256, 256): could not allocate 262144 bytes for 68th
> > slice
> >
> >
> > Cannot allocate memory
> > Darwin 550D-UOM88670.local 10.8.0 Darwin Kernel Version 10.8.0: Tue
> > Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
> >
> >
> > recon-all -s KSx3 exited with ERRORS at Mon Jul 23 10:15:13 EST 2012
> >
> >
> > For more details, see the log
> > file /Applications/freesurfer/subjects/KSx3/scripts/recon-all.log
> > To report a problem, see
> > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> >
> >
> > I would be grateful for any advice.
> >
> >
> > Regards,
> >
> >
> > EA Bowman
> >
> >
> >
> >
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