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?
2. Is this plan a good one?
3. Should I try and download another linux virtual box somewhere and put the version 6 beta on that?
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:
Does anyone have an idea of how I would go about deleting theoriginal 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).
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.
Should I try and download another linux virtual box somewhere andput 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
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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of zkaufman@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:
Does anyone have an idea of how I would go about deleting theoriginal 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).
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.
Should I try and download another linux virtual box somewhere andput 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.
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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of zkaufman@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:
Does anyone have an idea of how I would go about deleting theoriginal 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).
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.
Should I try and download another linux virtual box somewhere andput 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@nmr.mgh.harvard.edu
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Jeffrey Crawford -
Z K -
zkaufman＠nmr.mgh.harvard.edu