Liz, a 64bit build is in the works. in the meantime, you can get a version of mri_robust_register built for lion (64b) here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-lion/ Nick On Tue, 2012-10-02 at 12:12 -0400, Martin Reuter wrote: > 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: mreu...@nmr.mgh.harvard.edu > > To: ea_bow...@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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
