Hi Liz,
 
I have no idea about the progress of FS on 64 bit OSX. I think it should be possible to run Linux in a virtual box. Both these questions can probably be answered by Nick.
 
But I would recommend to first try to use a new version of mri_robust_template from our dev version (if it goes through, please double check 1 or two cases that the base norm.mgz looks good in the base and that all time points are aligned in the long directories). It may work as the new version needs less memory and I think 3.5 Gig should be enough for 3 time points.
 
Nick, can you point Liz to where to download a mac version of the mri_robust_template from dev?
 
Thanks, Martin
----- Original Message -----
From: Liz Bowman
To: FreeSurfer List
Sent: Monday, October 01, 2012 10:04 PM
Subject: Re: [Freesurfer] More than two time-points in longitudinal base = Memory allocation error?

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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> > Freesurfer@nmr.mgh.harvard.edu
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>
>
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