"mri_convert" just starts the man page for mri_convert. I have been looking at other things and 3D view in FSL also crashes with a 2657 segmentation fault and a core dump. I think the problem is in the virtualized 3D driver or something like that. It seems that CentOS 6.4 does have some problems with 3D. I use the latest vboxadditions 4.2.16. I dont think the error is Freesurfer. But ill dig deeper. Thank you for your time.

Best regards Rune

On Wed, Jul 10, 2013 at 4:29 PM, Z K zkaufman@nmr.mgh.harvard.edu wrote:

Rune,

I have not seen this error before. Can you please type mri_convert on the command line and tell me what, if any, output is produced.

-Zeke

On 07/10/2013 05:14 AM, Rune Frandsen wrote: I have just installed Freesurfer and wanted to try tkmedit I get a Segfault error and it asked me to write to this mail.

The .xdebug_tkmedit is

tkmedit started: Wed Jul 10 10:53:23 2013

/usr/local/freesurfer/tktools/**tkmedit.bin

$Id: tkmedit.c,v 1.343 2011/03/01 01:41:22 nicks Exp $ $Name: stable5 $

Segfault Creating main window xDebug stack (length: 2) 01: main() 01: Creating main window 00: 00:

My system is a fresh install of CentOS 6.4 64bit installed in VirtualBox. The only other program installed is FSL. The base machine is a HP Envy dv6 i7 16GB with Win8 64bit.

Is this a known problem?

Best regards Rune Frandsen (MD, phd student) Danish Center for Sleep Medicine runefrandsen@gmail.com

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/**compliancelinehttp://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.

I support what Marcos found. Freesurfer does not work on CentOS in VirtualBox because of the 3D error in the VirtualBox driver for graphics under CentOS. I solved the problem by using Vmware player instead. It seems more mature in the 3D driver. If others would like to use freesurfer on a virtualmachine i would recommend CentOS on Vmware player. I had the problem with Freesurfer 5,3, VirtualBox 4.2.16 with the adons 4.2.16_86992. When using ubuntu i have had some errors in FSL. So i would stick to CentOS on Vmware if you need to run on a windows 8 64bit machine

Best regards

On Tue, Jul 16, 2013 at 3:44 PM, Marcos Martins da Silva < marcosm@hucff.ufrj.br> wrote:

**

Hi, Rune and Zeke I have posted some time ago my experience with VirtualBox. I also got similar segfaults. The only way I could run FreeSurfer without problems was installing CentOS64 on a second hard disk so I have a dual boot system and skipped VirtualBox. Freesurfer 5.3 also solved some problems with recent Linux distributions related to the newest glibc. So if you have a linux system you can try to run FreeSurfer over it (Fedora works for sure and it seems several in this list uses Ubuntu). In my opinion the problem is related to VirtualBox itself, not the host neither the guest system. Cheers, Marcos Em Qui, 2013-07-11 às 10:57 +0200, Rune Frandsen escreveu:

"mri_convert" just starts the man page for mri_convert.

I have been looking at other things and 3D view in FSL also crashes with a 2657 segmentation fault and a core dump. I think the problem is in the virtualized 3D driver or something like that. It seems that CentOS 6.4 does have some problems with 3D. I use the latest vboxadditions 4.2.16. I dont think the error is Freesurfer. But ill dig deeper. Thank you for your time.

Best regards Rune

On Wed, Jul 10, 2013 at 4:29 PM, Z K zkaufman@nmr.mgh.harvard.edu wrote:

Rune,

I have not seen this error before. Can you please type mri_convert on the command line and tell me what, if any, output is produced.

-Zeke

On 07/10/2013 05:14 AM, Rune Frandsen wrote: I have just installed Freesurfer and wanted to try tkmedit I get a Segfault error and it asked me to write to this mail.

The .xdebug_tkmedit is

tkmedit started: Wed Jul 10 10:53:23 2013

/usr/local/freesurfer/tktools/tkmedit.bin

$Id: tkmedit.c,v 1.343 2011/03/01 01:41:22 nicks Exp $ $Name: stable5 $

Segfault Creating main window xDebug stack (length: 2) 01: main() 01: Creating main window 00: 00:

My system is a fresh install of CentOS 6.4 64bit installed in VirtualBox. The only other program installed is FSL. The base machine is a HP Envy dv6 i7 16GB with Win8 64bit.

Is this a known problem?

Best regards Rune Frandsen (MD, phd student) Danish Center for Sleep Medicine runefrandsen@gmail.com

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/ http://www.partners.org/complianceline complianceline 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.

-- Rune Frandsen runefrandsen@gmail.com

---

Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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

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.