Hi Everyone, I thought I would try installing FreeSurfer on Ubuntu because I was having so many issues trying to install Octave on CentOS. On the bright side, Ubuntu can download Octave directly from the repository. The downside is when I test my freesurfer install with tkmedit bert orig,mgz, I get the following error:
/usr/local/freesurfer/tktools/tksurfer.bin: Exec format error. Binary file not executable.
Is there is something additional I need to install because it is on Ubuntu?
Brian James Technical Applications Analyst North Bay Regional Health Centrehttp://www.nbrhc.on.ca/ (705) 474-8600 x2611
The information contained in this electronic transmission is intended for the person(s) or entity to whom it is addressed. Delivery of this message to any person other than the intended recipient(s) is not intended in any way to waive confidentiality. This material may contain confidential or personal information which may be subject to the provisions of Ontario's Personal Health Information Protection Act. Any review, retransmission, dissemination or other use of this information by entities other than the intended recipient is prohibited. If you receive this in error, please contact the sender and delete the material immediately.
L'information contenue dans ce message ?lectronique est destin?e uniquement au destinataire ou aux destinataires vis?s. La transmission de ce message ? une personne autre que son destinataire ou ses destinataires vis?s ne supprime en rien l'obligation d'en respecter la confidentialit?. Ce message peut contenir des renseignements de nature confidentielle ou personnelle qui pourraient ?tre soumis aux dispositions de la Loi de 2004 sur la protection des renseignements personnels sur la sant?. L'examen, la retransmission, la diffusion et toute autre utilisation de l'information contenue dans ce message par des personnes autres que le destinataire ou les destinataires vis?s sont interdits. Si vous recevez ce message par erreur, veuillez le supprimer imm?diatement et en avertir l'exp?diteur.
Just untarring the .tar.gz in /usr/local like documented here (http://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall) works like a charm on Ubuntu 11.10.
Best,
Martijn
Van: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Namens James, Brian Verzonden: vrijdag 30 december 2011 21:13 Aan: freesurfer@nmr.mgh.harvard.edu Onderwerp: [Freesurfer] FreeSurfer & Ubuntu 11.10
Hi Everyone,
I thought I would try installing FreeSurfer on Ubuntu because I was having so many issues trying to install Octave on CentOS. On the bright side, Ubuntu can download Octave directly from the repository. The downside is when I test my freesurfer install with tkmedit bert orig,mgz, I get the following error:
/usr/local/freesurfer/tktools/tksurfer.bin: Exec format error. Binary file not executable.
Is there is something additional I need to install because it is on Ubuntu?
Brian James
Technical Applications Analyst
North Bay Regional Health Centre http://www.nbrhc.on.ca/
(705) 474-8600 x2611
The information contained in this electronic transmission is intended for the person(s) or entity to whom it is addressed. Delivery of this message to any person other than the intended recipient(s) is not intended in any way to waive confidentiality. This material may contain confidential or personal information which may be subject to the provisions of Ontario's Personal Health Information Protection Act. Any review, retransmission, dissemination or other use of this information by entities other than the intended recipient is prohibited. If you receive this in error, please contact the sender and delete the material immediately.
L'information contenue dans ce message électronique est destinée uniquement au destinataire ou aux destinataires visés. La transmission de ce message à une personne autre que son destinataire ou ses destinataires visés ne supprime en rien l'obligation d'en respecter la confidentialité. Ce message peut contenir des renseignements de nature confidentielle ou personnelle qui pourraient être soumis aux dispositions de la Loi de 2004 sur la protection des renseignements personnels sur la santé. L'examen, la retransmission, la diffusion et toute autre utilisation de l'information contenue dans ce message par des personnes autres que le destinataire ou les destinataires visés sont interdits. Si vous recevez ce message par erreur, veuillez le supprimer immédiatement et en avertir l'expéditeur.
That is what I did...my path is /usr/local/freesurfer
However, mine doesn't seem to work.
Brian.
From: Martijn Steenwijk [mailto:martijnsteenwijk@gmail.com] Sent: December-30-11 2:37 PM To: James, Brian Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] FreeSurfer & Ubuntu 11.10
Just untarring the .tar.gz in /usr/local like documented here (http://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall) works like a charm on Ubuntu 11.10.
Best, Martijn
Van: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Namens James, Brian Verzonden: vrijdag 30 december 2011 21:13 Aan: freesurfer@nmr.mgh.harvard.edu Onderwerp: [Freesurfer] FreeSurfer & Ubuntu 11.10
Hi Everyone, I thought I would try installing FreeSurfer on Ubuntu because I was having so many issues trying to install Octave on CentOS. On the bright side, Ubuntu can download Octave directly from the repository. The downside is when I test my freesurfer install with tkmedit bert orig,mgz, I get the following error:
/usr/local/freesurfer/tktools/tksurfer.bin: Exec format error. Binary file not executable.
Is there is something additional I need to install because it is on Ubuntu?
Brian James Technical Applications Analyst North Bay Regional Health Centrehttp://www.nbrhc.on.ca/ (705) 474-8600 x2611
The information contained in this electronic transmission is intended for the person(s) or entity to whom it is addressed. Delivery of this message to any person other than the intended recipient(s) is not intended in any way to waive confidentiality. This material may contain confidential or personal information which may be subject to the provisions of Ontario's Personal Health Information Protection Act. Any review, retransmission, dissemination or other use of this information by entities other than the intended recipient is prohibited. If you receive this in error, please contact the sender and delete the material immediately.
L'information contenue dans ce message électronique est destinée uniquement au destinataire ou aux destinataires visés. La transmission de ce message à une personne autre que son destinataire ou ses destinataires visés ne supprime en rien l'obligation d'en respecter la confidentialité. Ce message peut contenir des renseignements de nature confidentielle ou personnelle qui pourraient être soumis aux dispositions de la Loi de 2004 sur la protection des renseignements personnels sur la santé. L'examen, la retransmission, la diffusion et toute autre utilisation de l'information contenue dans ce message par des personnes autres que le destinataire ou les destinataires visés sont interdits. Si vous recevez ce message par erreur, veuillez le supprimer immédiatement et en avertir l'expéditeur.
The information contained in this electronic transmission is intended for the person(s) or entity to whom it is addressed. Delivery of this message to any person other than the intended recipient(s) is not intended in any way to waive confidentiality. This material may contain confidential or personal information which may be subject to the provisions of Ontario's Personal Health Information Protection Act. Any review, retransmission, dissemination or other use of this information by entities other than the intended recipient is prohibited. If you receive this in error, please contact the sender and delete the material immediately.
L'information contenue dans ce message électronique est destinée uniquement au destinataire ou aux destinataires visés. La transmission de ce message à une personne autre que son destinataire ou ses destinataires visés ne supprime en rien l'obligation d'en respecter la confidentialité. Ce message peut contenir des renseignements de nature confidentielle ou personnelle qui pourraient être soumis aux dispositions de la Loi de 2004 sur la protection des renseignements personnels sur la santé. L'examen, la retransmission, la diffusion et toute autre utilisation de l'information contenue dans ce message par des personnes autres que le destinataire ou les destinataires visés sont interdits. Si vous recevez ce message par erreur, veuillez le supprimer immédiatement et en avertir l'expéditeur.
Hi Brian
I had to change the terminal config for it to use tcsh.
I think Ubuntu now uses The Debian Almquist shell (dash) and I have had problems running freesurfer from it.
install tcsh using aptitude and then in the preferences of your terminal (Edit > profile preferences) in the tab "title and command" click on "run custom command instead of my shell" and type /bin/tcsh as your custom command.
You can also set up some environment variables by editing the .tcshrc found in your home directory.
gedit ~/.tcshrc
and add a modified version of this code according to where your freesurfer install is and where your subject directory lies...
alias freesurfer 'setenv FREESURFER_HOME /usr/local/freesurfer; setenv SUBJECTS_DIR ~/subjects; source $FREESURFER_HOME/SetUpFreeSurfer.csh'
now if you close your terminal and open a new one, freesurfer should work.
Hope it helps
Ian
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of James, Brian [Brian.James@nbrhc.on.ca] Sent: 30 December 2011 20:40 To: martijnsteenwijk@gmail.com Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FreeSurfer & Ubuntu 11.10
That is what I did…my path is /usr/local/freesurfer
However, mine doesn’t seem to work.
Brian.
From: Martijn Steenwijk [mailto:martijnsteenwijk@gmail.com] Sent: December-30-11 2:37 PM To: James, Brian Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] FreeSurfer & Ubuntu 11.10
Just untarring the .tar.gz in /usr/local like documented here (http://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall) works like a charm on Ubuntu 11.10.
Best, Martijn
Van: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Namens James, Brian Verzonden: vrijdag 30 december 2011 21:13 Aan: freesurfer@nmr.mgh.harvard.edu Onderwerp: [Freesurfer] FreeSurfer & Ubuntu 11.10
Hi Everyone, I thought I would try installing FreeSurfer on Ubuntu because I was having so many issues trying to install Octave on CentOS. On the bright side, Ubuntu can download Octave directly from the repository. The downside is when I test my freesurfer install with tkmedit bert orig,mgz, I get the following error:
/usr/local/freesurfer/tktools/tksurfer.bin: Exec format error. Binary file not executable.
Is there is something additional I need to install because it is on Ubuntu?
Brian James Technical Applications Analyst North Bay Regional Health Centrehttp://www.nbrhc.on.ca/ (705) 474-8600 x2611
The information contained in this electronic transmission is intended for the person(s) or entity to whom it is addressed. Delivery of this message to any person other than the intended recipient(s) is not intended in any way to waive confidentiality. This material may contain confidential or personal information which may be subject to the provisions of Ontario's Personal Health Information Protection Act. Any review, retransmission, dissemination or other use of this information by entities other than the intended recipient is prohibited. If you receive this in error, please contact the sender and delete the material immediately.
L'information contenue dans ce message électronique est destinée uniquement au destinataire ou aux destinataires visés. La transmission de ce message à une personne autre que son destinataire ou ses destinataires visés ne supprime en rien l'obligation d'en respecter la confidentialité. Ce message peut contenir des renseignements de nature confidentielle ou personnelle qui pourraient être soumis aux dispositions de la Loi de 2004 sur la protection des renseignements personnels sur la santé. L'examen, la retransmission, la diffusion et toute autre utilisation de l'information contenue dans ce message par des personnes autres que le destinataire ou les destinataires visés sont interdits. Si vous recevez ce message par erreur, veuillez le supprimer immédiatement et en avertir l'expéditeur.
The information contained in this electronic transmission is intended for the person(s) or entity to whom it is addressed. Delivery of this message to any person other than the intended recipient(s) is not intended in any way to waive confidentiality. This material may contain confidential or personal information which may be subject to the provisions of Ontario's Personal Health Information Protection Act. Any review, retransmission, dissemination or other use of this information by entities other than the intended recipient is prohibited. If you receive this in error, please contact the sender and delete the material immediately.
L'information contenue dans ce message électronique est destinée uniquement au destinataire ou aux destinataires visés. La transmission de ce message à une personne autre que son destinataire ou ses destinataires visés ne supprime en rien l'obligation d'en respecter la confidentialité. Ce message peut contenir des renseignements de nature confidentielle ou personnelle qui pourraient être soumis aux dispositions de la Loi de 2004 sur la protection des renseignements personnels sur la santé. L'examen, la retransmission, la diffusion et toute autre utilisation de l'information contenue dans ce message par des personnes autres que le destinataire ou les destinataires visés sont interdits. Si vous recevez ce message par erreur, veuillez le supprimer immédiatement et en avertir l'expéditeur.
Hi Ian, Thanks for the information. So I followed your instructions carefully with the same result (I modified the terminal options as well). I also modified it as well to see if I can get it working but to no avail. Here is the contents of my .tcshrc file:
#.tcshrc
# User specific aliases and functions
alias rm 'rm -i' alias cp 'cp -i' alias mv 'mv -i' alias freesurfer 'setenv FREESURFER_HOME /usr/local/freesurfer; setenv SUBJECTS_DIR /usr/local/freesurfer/subjects; source $FREESURFER_HOME/SetUpFreeSurfer.csh'
set prompt='[%n@%m %c]# '
setenv FREESURFER_HOME /usr/local/freesurfer setenv SUBJECTS_DIR /usr/local/freesurfer/subjects source $FREESURFER_HOME/SetUpFreeSurfer.csh
Here is what my terminal looks like: Which looks correct to me....
-------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni [root@brian-Latitude-E6410 ~]# tkmedit bert config.mgz /usr/local/freesurfer/tktools/tkmedit.bin: Exec format error. Binary file not executable.
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ian Charest [Ian.Charest@mrc-cbu.cam.ac.uk] Sent: December-30-11 7:43 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FreeSurfer & Ubuntu 11.10
Hi Brian
I had to change the terminal config for it to use tcsh.
I think Ubuntu now uses The Debian Almquist shell (dash) and I have had problems running freesurfer from it.
install tcsh using aptitude and then in the preferences of your terminal (Edit > profile preferences) in the tab "title and command" click on "run custom command instead of my shell" and type /bin/tcsh as your custom command.
You can also set up some environment variables by editing the .tcshrc found in your home directory.
gedit ~/.tcshrc
and add a modified version of this code according to where your freesurfer install is and where your subject directory lies...
alias freesurfer 'setenv FREESURFER_HOME /usr/local/freesurfer; setenv SUBJECTS_DIR ~/subjects; source $FREESURFER_HOME/SetUpFreeSurfer.csh'
now if you close your terminal and open a new one, freesurfer should work.
Hope it helps
Ian
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of James, Brian [Brian.James@nbrhc.on.ca] Sent: 30 December 2011 20:40 To: martijnsteenwijk@gmail.com Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FreeSurfer & Ubuntu 11.10
That is what I did…my path is /usr/local/freesurfer
However, mine doesn’t seem to work.
Brian.
From: Martijn Steenwijk [mailto:martijnsteenwijk@gmail.com] Sent: December-30-11 2:37 PM To: James, Brian Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] FreeSurfer & Ubuntu 11.10
Just untarring the .tar.gz in /usr/local like documented here (http://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall) works like a charm on Ubuntu 11.10.
Best, Martijn
Van: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Namens James, Brian Verzonden: vrijdag 30 december 2011 21:13 Aan: freesurfer@nmr.mgh.harvard.edu Onderwerp: [Freesurfer] FreeSurfer & Ubuntu 11.10
Hi Everyone, I thought I would try installing FreeSurfer on Ubuntu because I was having so many issues trying to install Octave on CentOS. On the bright side, Ubuntu can download Octave directly from the repository. The downside is when I test my freesurfer install with tkmedit bert orig,mgz, I get the following error:
/usr/local/freesurfer/tktools/tksurfer.bin: Exec format error. Binary file not executable.
Is there is something additional I need to install because it is on Ubuntu?
Brian James Technical Applications Analyst North Bay Regional Health Centrehttp://www.nbrhc.on.ca/ (705) 474-8600 x2611
The information contained in this electronic transmission is intended for the person(s) or entity to whom it is addressed. Delivery of this message to any person other than the intended recipient(s) is not intended in any way to waive confidentiality. This material may contain confidential or personal information which may be subject to the provisions of Ontario's Personal Health Information Protection Act. Any review, retransmission, dissemination or other use of this information by entities other than the intended recipient is prohibited. If you receive this in error, please contact the sender and delete the material immediately.
L'information contenue dans ce message électronique est destinée uniquement au destinataire ou aux destinataires visés. La transmission de ce message à une personne autre que son destinataire ou ses destinataires visés ne supprime en rien l'obligation d'en respecter la confidentialité. Ce message peut contenir des renseignements de nature confidentielle ou personnelle qui pourraient être soumis aux dispositions de la Loi de 2004 sur la protection des renseignements personnels sur la santé. L'examen, la retransmission, la diffusion et toute autre utilisation de l'information contenue dans ce message par des personnes autres que le destinataire ou les destinataires visés sont interdits. Si vous recevez ce message par erreur, veuillez le supprimer immédiatement et en avertir l'expéditeur.
The information contained in this electronic transmission is intended for the person(s) or entity to whom it is addressed. Delivery of this message to any person other than the intended recipient(s) is not intended in any way to waive confidentiality. This material may contain confidential or personal information which may be subject to the provisions of Ontario's Personal Health Information Protection Act. Any review, retransmission, dissemination or other use of this information by entities other than the intended recipient is prohibited. If you receive this in error, please contact the sender and delete the material immediately.
L'information contenue dans ce message électronique est destinée uniquement au destinataire ou aux destinataires visés. La transmission de ce message à une personne autre que son destinataire ou ses destinataires visés ne supprime en rien l'obligation d'en respecter la confidentialité. Ce message peut contenir des renseignements de nature confidentielle ou personnelle qui pourraient être soumis aux dispositions de la Loi de 2004 sur la protection des renseignements personnels sur la santé. L'examen, la retransmission, la diffusion et toute autre utilisation de l'information contenue dans ce message par des personnes autres que le destinataire ou les destinataires visés sont interdits. Si vous recevez ce message par erreur, veuillez le supprimer immédiatement et en avertir l'expéditeur.
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L'information contenue dans ce message électronique est destinée uniquement au destinataire ou aux destinataires visés. La transmission de ce message à une personne autre que son destinataire ou ses destinataires visés ne supprime en rien l'obligation d'en respecter la confidentialité. Ce message peut contenir des renseignements de nature confidentielle ou personnelle qui pourraient être soumis aux dispositions de la Loi de 2004 sur la protection des renseignements personnels sur la santé. L'examen, la retransmission, la diffusion et toute autre utilisation de l'information contenue dans ce message par des personnes autres que le destinataire ou les destinataires visés sont interdits. Si vous recevez ce message par erreur, veuillez le supprimer immédiatement et en avertir l'expéditeur.
FS works fine on Ubuntu (11.10).
On 12/30/11 15:12, James, Brian wrote:
/usr/local/freesurfer/tktools/tksurfer.bin: Exec format error. Binary file not executable.
This error typically happens when you try and run a 64-bit executable on a 32-bit system. From your later posts, you are clearly running the 64-bit FS:
-------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 --------
The question now is, is your base system 32 or 64-bit?There are many ways to ascertain this. One simple one is to type
$>file /sbin/init
which on a 64 bit system returns:
/sbin/init: ELF 64-bit LSB shared object, x86-64, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.6.15, stripped
and on a 32-bit system returns:
/sbin/init: ELF 32-bit LSB shared object, Intel 80386, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.6.15, stripped
Please verify your base system "bit"ness.
Best -=R
Hi Rudolph You are correct. My version is 32 bit. How silly of me. When I get back to work on Tuesday I will install the 64 bit version of Ubuntu and let you guys know how it goes.
Thanks again to everyone for their suggestions. It is greatly appreciated.
Happy New Year!!
From: Rudolph Pienaar [mailto:rudolph@nmr.mgh.harvard.edu] Sent: Saturday, December 31, 2011 02:08 PM To: James, Brian Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FreeSurfer & Ubuntu 11.10
FS works fine on Ubuntu (11.10).
On 12/30/11 15:12, James, Brian wrote:
The information contained in this electronic transmission is intended for the person(s) or entity to whom it is addressed. Delivery of this message to any person other than the intended recipient(s) is not intended in any way to waive confidentiality. This material may contain confidential or personal information which may be subject to the provisions of Ontario's Personal Health Information Protection Act. Any review, retransmission, dissemination or other use of this information by entities other than the intended recipient is prohibited. If you receive this in error, please contact the sender and delete the material immediately.
L'information contenue dans ce message �lectronique est destin�e uniquement au destinataire ou aux destinataires vis�s. La transmission de ce message � une personne autre que son destinataire ou ses destinataires vis�s ne supprime en rien l'obligation d'en respecter la confidentialit�. Ce message peut contenir des renseignements de nature confidentielle ou personnelle qui pourraient �tre soumis aux dispositions de la Loi de 2004 sur la protection des renseignements personnels sur la sant�. L'examen, la retransmission, la diffusion et toute autre utilisation de l'information contenue dans ce message par des personnes autres que le destinataire ou les destinataires vis�s sont interdits. Si vous recevez ce message par erreur, veuillez le supprimer imm�diatement et en avertir l'exp�diteur.
freesurfer@nmr.mgh.harvard.edu
-
Ian Charest -
James, Brian -
Martijn Steenwijk -
Rudolph Pienaar