Hello, So yes, this is expected. The just checked and the freesurfer VirtualBox image is a 32bit operating system, and includes the 32bit version of freesurfer. (I vaguely recall that when I set this up 3.5 years ago there were no 64bit Ubuntu virtualbox images available.)
So the freesurfer v6-beta will not work on it because it's 64bit. We will not be distributing as 32bit of freesurfer. This means you will need to install the beta version on a 64bit VirtualBox image, which is widely available now, and included in the link I sent below. On 11/17/2016 03:03 PM, Jeffrey Crawford wrote: > So, I discovered that I could delete the files inside of the Freesurfer > folder, even though I could not delete the Freesurfer folder itself. However, > when I replaced the interior of the file with the version 6 folders, I got a > bunch of errors when I tried to run my first recon-all: > > "recon-all -s 2007 \ -i /media/drive/3T_BSNIP_subjects/2007.nii > > WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! > > Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-v6-beta-20161028-4cfbf2a > Current Stamp: freesurfer-Linux-centos6_x86_64-stable-v6-beta-20161028-4cfbf2a > INFO: SUBJECTS_DIR is /media/E_big_daddy_drive/3T_BSNIP_subjects > Actual FREESURFER_HOME /usr/local/freesurfer > Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 > UTC 2012 i686 i686 i386 GNU/Linux > /usr/local/freesurfer/bin/mri_convert: line 3: > /usr/local/freesurfer/bin/mri_convert.bin: cannot execute binary file > /usr/local/freesurfer/bin/flirt.fsl: Exec format error. Binary file not > executable. > /usr/local/freesurfer/bin/mri_convert: line 3: > /usr/local/freesurfer/bin/mri_convert.bin: cannot execute binary file > /usr/local/freesurfer/tktools/tkregister2_cmdl: Exec format error. > ..... > ...." > > The script continued on saying " Exec format error. Binary file not > executable" for the rest of the files in the V6 folders. > > I am sure this error is unique to my attempt at putting V6 on this 5.3 > virtual box, because I followed the exact same steps on the Linux we have and > everything worked fine. > > So, unless anyone has some ways for me to patch up this odd attempt of mine, > then I think I will just move on to a linux virtual box. I will take your > previously recommended link first and see how that helps. > > Thank you so much for your reply. > > > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of > zkauf...@nmr.mgh.harvard.edu > Sent: Thursday, November 17, 2016 12:10 PM > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Cc: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Version 6 Beta on Virtual Box problem > >> Hello everyone! >> >> I am currently using Virtual Box to run Freesurfer and I was wondering >> if my plan to put the version 6 beta on to my current virtual box was >> a valid one. >> >> My plan was to delete the Freesurfer folder off of the 5.3 virtual box >> and replace it with the Freesurfer version 6 folder. However, the >> virtual box is not letting me delete the Freesurfer folder. >> So I have some questions: >> >> 1. Does anyone have an idea of how I would go about deleting the >> original Freesurfer folder, so I could continue with this plan? > > Are you just getting a permissions error when you attempt to delete the > folder? I created that disk image with freesurfer installed on it, but I > would still think that the freesurfer folder could be deleted. Recall that > the root password for the disk image is 'freesurfer' (without the quotes). > >> 2. Is this plan a good one? > > Its a workable plan. The Virtual Box version of freesurfer has its > limitations, but if it works for you than this plan seems adequate for > testing purposes. > >> >> 3. Should I try and download another linux virtual box somewhere and >> put the version 6 beta on that? > > This would be my suggestion. Try just installing any of the Ubuntu disk > images and installing freesurfer within that > (http://www.osboxes.org/ubuntu/) > > > >> _______________________________________________ >> 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
