[Freesurfer] recon-all problems [solved]
I had several problems testing freesurfer 5.2 installation, as previously posted. Now it is all OK and I would like to share what I could learn: 1- It does not work on Fedora 18 (segfaults with all tests with tkmedit, tksurfer and recon-all) that is due to a restriction imposed by glibc (only newest version). Only freeview works under Fedora 18 but, even here, I got a misalignment problem among surfaces and volumes. More details at https://bugzilla.redhat.com/show_bug.cgi?id=905638 2- I got partial functionality using VirtualBox (4.2.8 and 4.2.10). I cannot say about previous versions and the latest one (4.2.12 was released on Apriil, 12th). But I had problems with both virtual machines I tried: CentOS6 (fresh install) and the Xubuntu + FreeSurfer 5.1 vdi file I downloaded from FreeSurfer website. Tkmedit, tksurfer and freeview all worked but recon-all failed all time. 3- Fedora 17 and CentOS 6 work flawlessly out of box if you do not use virtualbox. Probably, other distros will work too, except if they are using the latest glibc (2.16-30). So my final setup is a dual boot machine: Fedora 18 (day-by-day tasks) and CentOS6 (freesurfer tasks). You can do it with only one disk but it is a lot easier with two. I hope it can help people with similar problems. ___ 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] recon-all problems [solved]
I had several problems testing freesurfer 5.2 installation, as previously posted. Now it is all OK and I would like to share what I could learn: 1- It does not work on Fedora 18 (segfaults with all tests with tkmedit, tksurfer and recon-all) that is due to a restriction imposed by glibc (only newest version). Only freeview works under Fedora 18 but, even here, I got a misalignment problem among surfaces and volumes. More details at https://bugzilla.redhat.com/show_bug.cgi?id=905638 2- I got partial functionality using VirtualBox (4.2.8 and 4.2.10). I cannot say about previous versions and the latest one (4.2.12 was released on Apriil, 12th). But I had problems with both virtual machines I tried: CentOS6 (fresh install) and the Xubuntu + FreeSurfer 5.1 vdi file I downloaded from FreeSurfer website. Tkmedit, tksurfer and freeview all worked but recon-all failed all time. 3- Fedora 17 and CentOS 6 work flawlessly out of box if you do not use virtualbox. Probably, other distros will work too, except if they are using the latest glibc (2.16-30). So my final setup is a dual boot machine: Fedora 18 (day-by-day tasks) and CentOS6 (freesurfer tasks). You can do it with only one disk but it is a lot easier with two. I hope it can help people with similar problems. ___ 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.
Re: [Freesurfer] recon-all problems [solved]
Marcos, Thanks for looking into this. We dont have a Fedora 18 system to replicate the problem on, but we're looking at the section of code described in bugzilla report. We may need your help to test any fixes we devise. Nick On Mon, 2013-04-15 at 17:59 -0300, Marcos Martins da Silva wrote: > > I had several problems testing freesurfer 5.2 installation, as > previously posted. Now it is all OK and I would like to share what I > could learn: > > 1- It does not work on Fedora 18 (segfaults with all tests with > tkmedit, tksurfer and recon-all) that is due to a restriction imposed > by glibc (only newest version). Only freeview works under Fedora 18 > but, even here, I got a misalignment problem among surfaces and > volumes. More details at > https://bugzilla.redhat.com/show_bug.cgi?id=905638 > 2- I got partial functionality using VirtualBox (4.2.8 and 4.2.10). I > cannot say about previous versions and the latest one (4.2.12 was > released on Apriil, 12th). But I had problems with both virtual > machines I tried: CentOS6 (fresh install) and the Xubuntu + FreeSurfer > 5.1 vdi file I downloaded from FreeSurfer website. Tkmedit, tksurfer > and freeview all worked but recon-all failed all time. > 3- Fedora 17 and CentOS 6 work flawlessly out of box if you do not use > virtualbox. Probably, other distros will work too, except if they are > using the latest glibc (2.16-30). So my final setup is a dual boot > machine: Fedora 18 (day-by-day tasks) and CentOS6 (freesurfer tasks). > You can do it with only one disk but it is a lot easier with two. > > I hope it can help people with similar problems. > ___ > 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.
Re: [Freesurfer] recon-all problems [solved]
Marcos, Can you give this version of tkmedit a try on your Fedora 18 system? ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/ you will need to copy tkmedit.bin to your freesurfer/tktools directory (not the freesurfer/bin directory). you may need to type this to make it executable: chmod a+x tkmedit.bin it contains a potential fix to the problem (but i dont have a way to replicate the error to test it). Nick On Mon, 2013-04-15 at 18:02 -0400, Nick Schmansky wrote: > Marcos, > > Thanks for looking into this. We dont have a Fedora 18 system to > replicate the problem on, but we're looking at the section of code > described in bugzilla report. We may need your help to test any fixes > we devise. > > Nick > > > On Mon, 2013-04-15 at 17:59 -0300, Marcos Martins da Silva wrote: > > > > I had several problems testing freesurfer 5.2 installation, as > > previously posted. Now it is all OK and I would like to share what I > > could learn: > > > > 1- It does not work on Fedora 18 (segfaults with all tests with > > tkmedit, tksurfer and recon-all) that is due to a restriction imposed > > by glibc (only newest version). Only freeview works under Fedora 18 > > but, even here, I got a misalignment problem among surfaces and > > volumes. More details at > > https://bugzilla.redhat.com/show_bug.cgi?id=905638 > > 2- I got partial functionality using VirtualBox (4.2.8 and 4.2.10). I > > cannot say about previous versions and the latest one (4.2.12 was > > released on Apriil, 12th). But I had problems with both virtual > > machines I tried: CentOS6 (fresh install) and the Xubuntu + FreeSurfer > > 5.1 vdi file I downloaded from FreeSurfer website. Tkmedit, tksurfer > > and freeview all worked but recon-all failed all time. > > 3- Fedora 17 and CentOS 6 work flawlessly out of box if you do not use > > virtualbox. Probably, other distros will work too, except if they are > > using the latest glibc (2.16-30). So my final setup is a dual boot > > machine: Fedora 18 (day-by-day tasks) and CentOS6 (freesurfer tasks). > > You can do it with only one disk but it is a lot easier with two. > > > > I hope it can help people with similar problems. > > ___ > > 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 > > ___ 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.
