New subject: More than two time-points in longitudinal base = Memory allocation error?

22 Jul 2012

    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
    > > 
    > > 
    > > 
    > > 
    > > _______________________________________________
    > > Freesurfer mailing list
    > > Freesurfer@nmr.mgh.harvard.edu
    > >
    https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
    > 
    > 
    > _______________________________________________
    > Freesurfer mailing list
    > Freesurfer@nmr.mgh.harvard.edu
    > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
    > 
    > 
    > The information in this e-mail is intended only for the
    person to whom it is
    > addressed. If you believe this e-mail was sent to you in
    error and the e-mail
    > contains patient information, please contact the Partners
    Compliance HelpLine at
    > http://www.partners.org/complianceline . If the e-mail was
    sent to you in error
    > but does not contain patient information, please contact the
    sender and properly
    > dispose of the e-mail.
    > 


    ______________________________________________________________

    _______________________________________________
    Freesurfer mailing list
    Freesurfer@nmr.mgh.harvard.edu
    https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer