Hello.
I am going to attempt to install FS on Ubuntu, but just had a quick question before I start. On the Download page on the wiki site, it states the following:
On Ubuntu, you will need to do the following: cd /usr/lib ln -s libtiff.so.4 libtiff.so.3
When exactly does this need to be done? I know this probably sounds like a really stupid question, but I have had major issues with installing FS and want to make sure I know exactly what needs doing and when it needs to be done. So I'd really appreciate some insight. Thank you.
Kind regards, Fatima
Just do it before you try to run any of the FreeSurfer programs. What issues are you having? I have FreeSurfer installed on a number of Ubuntu machines.
Peace,
Matt.
_____
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Ahmed, F, Me fahmed@sun.ac.za Sent: Monday, August 24, 2009 5:21 AM To: Freesurfer Mailing List Subject: [Freesurfer] installing on ubuntu
Hello.
I am going to attempt to install FS on Ubuntu, but just had a quick question before I start. On the Download page on the wiki site, it states the following:
On Ubuntu, you will need to do the following:
cd /usr/lib
ln -s libtiff.so.4 libtiff.so.3
When exactly does this need to be done? I know this probably sounds like a really stupid question, but I have had major issues with installing FS and want to make sure I know exactly what needs doing and when it needs to be done. So I'd really appreciate some insight. Thank you.
Kind regards,
Fatima
Hi Matt,
The problems I've been having with Freesurfer are endless lol. I can't figure out how to get it installed on my CentOS Linux. The tar.gz extraction doesn't work so I can't get it installed. So, that command doesn't have to be used in installation? I am SO bad at Linux it's unbelievable. Thanks for that though.
Fatima
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Matt Glasser Sent: 24 August 2009 14:31 To: fahmed@sun.ac.za Cc: 'Freesurfer Mailing List' Subject: Re: [Freesurfer] installing on ubuntu
Just do it before you try to run any of the FreeSurfer programs. What issues are you having? I have FreeSurfer installed on a number of Ubuntu machines.
Peace,
Matt.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Ahmed, F, Me fahmed@sun.ac.za Sent: Monday, August 24, 2009 5:21 AM To: Freesurfer Mailing List Subject: [Freesurfer] installing on ubuntu
Hello.
I am going to attempt to install FS on Ubuntu, but just had a quick question before I start. On the Download page on the wiki site, it states the following:
On Ubuntu, you will need to do the following: cd /usr/lib ln -s libtiff.so.4 libtiff.so.3
When exactly does this need to be done? I know this probably sounds like a really stupid question, but I have had major issues with installing FS and want to make sure I know exactly what needs doing and when it needs to be done. So I'd really appreciate some insight. Thank you.
Kind regards, Fatima
Ahmed, F, Me fahmed@sun.ac.za wrote:
On Ubuntu, you will need to do the following: cd /usr/lib ln -s libtiff.so.4 libtiff.so.3
Actually, you should probably use:
sudo ln -s /usr/lib/libtiff.so.4 /usr/lib/lib/tiff.so.3
(it amounts to the same thing, but this way is just one line that you can simply cut-and-paste. The system will prompt you for your password.
Also the 'ubuntu' way is to use 'sudo' for administrator-type operations. If you just use the above, you will probably get 'Permission denied errors').
Note that you *might* get other missing dependencies -- especially if you are on a freshly installed ubuntu machine. They are relatively easy to resolve using 'apt-get'
When exactly does this need to be done? I know this probably sounds like a really stupid question, but I have had major issues with installing FS and want to make sure I know exactly what needs doing and when it needs to be done. So I’d really appreciate some insight. Thank you.
It doesn't matter when you do it -- either before or after you unpack the archive. Just make sure to do it before you actually run any FreeSurfer GUI type apps. If you forget to do it, you'll simply get an error along the lines of 'libtiff.so.3 not found'
I assume you meant sudo ln -s /usr/lib/libtiff.so.4 /usr/lib/libtiff.so.3
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Rudolph Pienaar Sent: Monday, August 24, 2009 10:04 AM To: Ahmed, F, Me fahmed@sun.ac.za Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] installing on ubuntu
Ahmed, F, Me fahmed@sun.ac.za wrote:
On Ubuntu, you will need to do the following: cd /usr/lib ln -s libtiff.so.4 libtiff.so.3
Actually, you should probably use:
sudo ln -s /usr/lib/libtiff.so.4 /usr/lib/lib/tiff.so.3
(it amounts to the same thing, but this way is just one line that you can simply cut-and-paste. The system will prompt you for your password.
Also the 'ubuntu' way is to use 'sudo' for administrator-type operations. If you just use the above, you will probably get 'Permission denied errors').
Note that you *might* get other missing dependencies -- especially if you are on a freshly installed ubuntu machine. They are relatively easy to resolve using 'apt-get'
When exactly does this need to be done? I know this probably sounds like a really stupid question, but I have had major issues with installing FS and want to make sure I know exactly what needs doing and when it needs to be done. So I'd really appreciate some insight. Thank you.
It doesn't matter when you do it -- either before or after you unpack the archive. Just make sure to do it before you actually run any FreeSurfer GUI type apps. If you forget to do it, you'll simply get an error along the lines of 'libtiff.so.3 not found'
Matt Glasser wrote:
I assume you meant sudo ln -s /usr/lib/libtiff.so.4 /usr/lib/libtiff.so.3
Yes - thanks!
Fatima,
The current release, v4.5.0, no longer requires performing the 'libtiff' link. What other issues are you encountering?
Nick
On Mon, 2009-08-24 at 12:20 +0200, Ahmed, F, Me wrote:
Hello.
I am going to attempt to install FS on Ubuntu, but just had a quick question before I start. On the Download page on the wiki site, it states the following:
On Ubuntu, you will need to do the following: cd /usr/lib ln -s libtiff.so.4 libtiff.so.3
When exactly does this need to be done? I know this probably sounds like a really stupid question, but I have had major issues with installing FS and want to make sure I know exactly what needs doing and when it needs to be done. So I’d really appreciate some insight. Thank you.
Kind regards, Fatima
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I just did a fresh install of 4.5.0 on a new machine with an "out of the box" Ubuntu 9.04....
You still need (at least):
* to create the symbolic link for libtiff * to install the tcsh package (wich is not by default)
Hope this can help.
-----------------------------------------------------------------------------------------------------------------------------------
Dr Philippe Feuerstein Radiologie Groupe Hospitalier du Centre Alsace Hôpital Albert Schweitzer 201, Avenue d'Alsace - BP 20129 68003 Colmar Cedex France
Tél: +33 3 89 21 25 74
mailto: philippe.feuerstein@ghca.fr
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Nick Schmansky Sent: Monday, August 24, 2009 9:20 PM To: Ahmed, F, Me fahmed@sun.ac.za Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] installing on ubuntu
Fatima,
The current release, v4.5.0, no longer requires performing the 'libtiff' link. What other issues are you encountering?
Nick
On Mon, 2009-08-24 at 12:20 +0200, Ahmed, F, Me wrote:
Hello.
I am going to attempt to install FS on Ubuntu, but just had a quick question before I start. On the Download page on the wiki site, it states the following:
On Ubuntu, you will need to do the following: cd /usr/lib ln -s libtiff.so.4 libtiff.so.3
When exactly does this need to be done? I know this probably sounds like a really stupid question, but I have had major issues with installing FS and want to make sure I know exactly what needs doing and when it needs to be done. So I'd really appreciate some insight. Thank you.
Kind regards, Fatima
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
Hi Nick,
You probably don't recall but you were trying to help me sort out a few problems with my FS a while back. You told me to uninstall and then reinstall to hopefully see if the problem fixes itself. The problems I face now are with the installation, I followed the commands on the wiki site for installation and carried out this command:
tar tzf freesurfer-Linux-<platform>-<release>-full.tar.gz
this then showed the contents of the tar.gz file, I saw those all perfectly fine and then I moved onto the next command:
cd /usr/local tar xzvf freesurfer-Linux-<platform>-<release>-full.tar.gz
and I got the following error:
tar: freesurfer-Linux-centos4-stable-pub-v4.3.1-full.tar: Cannot
open: No such file or directory
tar: Error is not recoverable: exiting now
tar: Child returned status 2
tar: Error exit delayed from previous errors
Pedro and Allison tried to help, and I then found that I don't have permission to write in the /usr/local directory.
Fatima
-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: 24 August 2009 21:20 To: Ahmed, F, Me fahmed@sun.ac.za Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] installing on ubuntu
Fatima,
The current release, v4.5.0, no longer requires performing the 'libtiff' link. What other issues are you encountering?
Nick
On Mon, 2009-08-24 at 12:20 +0200, Ahmed, F, Me wrote:
Hello.
I am going to attempt to install FS on Ubuntu, but just had a quick question before I start. On the Download page on the wiki site, it states the following:
On Ubuntu, you will need to do the following: cd /usr/lib ln -s libtiff.so.4 libtiff.so.3
When exactly does this need to be done? I know this probably sounds like a really stupid question, but I have had major issues with installing FS and want to make sure I know exactly what needs doing and when it needs to be done. So I’d really appreciate some insight. Thank you.
Kind regards, Fatima
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Fatima --
Ahmed, F, Me fahmed@sun.ac.za wrote:
cd /usr/local tar xzvf freesurfer-Linux-<platform>-<release>-full.tar.gz
and I got the following error:
tar: freesurfer-Linux-centos4-stable-pub-v4.3.1-full.tar: Cannot
open: No such file or directory
That error in fact does make sense. The 'tar' command is trying to unpack the archive, but it is saying that it can't find the archive file. That most likely is because the archive file is *not* in the /usr/local folder (or directory).
I'm guessing that you downloaded the archive to your Desktop -- this is usually the case if you use 'firefox' to download. Assuming that to be the case, the *full* path to the archive is:
/home/fatima/Desktop/freesurfer-Linux-centos4-stable-pub-v4.3.1-full.tar
(assuming that your user name on your computer is 'fatima'). Sometimes 'firefox' might download to your 'Downloads' folder:
/home/fatima/Downloads/freesurfer-Linux-centos4-stable-pub-v4.3.1-full.tar
I'm going to assume the archive is on your Desktop since this is the most common. Now, in order to install, you need to make sure about two things:
1. That you properly specify the archive. 2. That you have permissions to unpack the archive.
When you login, you have permission to read/write files and folders only in your "home" folder, i.e. /home/fatima -- anywhere "outside" this, and you will probably need administrator permission. This administrator is typically called 'root' on Linux/Mac/Unix systems.
On a CentOS box, when you want to install, you should change your user to 'root'. This means typing:
$>su
The prompt will ask you for a password. This is the 'root' password and was setup by whomever setup your computer. This password is probably not the same as your, i.e. 'fatima', password. When you have done that, you will notice that the prompt has changed slightly:
#>
i.e., the '$' is now '#', signifying that you are now 'root'.
Now, assuming that the freesurfer archive is still in your (i.e. 'fatima's) Desktop, you should try:
$>su Password: <type root password> #>cd /usr/local #>tar xzvf /home/fatima/Desktop/freesurfer-Linux-centos4-stable-pub-v4.3.1-full.tar
and you should hopefully be all set. By the way, you don't need to type every single character in the name. Just type the first one or two and then press <tab>. The shell will fill in the rest as far as it can. So when you start typing '/home/fa' press <tab> and it will automatically fill out '/home/fatima'. Then continue typing '/Des' and press <tab> -- you will see '/home/fatima/Desktop'. Now continue and type '/free' and press <tab> then the whole 'freesurfer-Linux-centos4-stable-pub-v4.3.1-full.tar' will automatically be completed.
On Ubuntu, it's pretty much the same as CentOS, but we use 'sudo' instead of 'su', and you can use your password and not the 'root' password:
$>sudo bash Password: <type YOUR password> #>cd /usr/local #>tar xzvf /home/fatima/Desktop/freesurfer-Linux-centos4-stable-pub-v4.3.1-full.tar
in both cases, when you're done unpacking, simply type: 'exit' so that you are no longer the 'root' user and return to being 'fatima'.
HTH -=R
Hi Rudolph,
Sorry for the late reply, was busy at work yesterday. Wow, your explanations are so incredibly clear and you explain things so easily, thank you! It really helps when I know NOTHING about Linux. I'm going to try what you said below and see if that helps and then will let you know. So thanks once again.
Fatima
-----Original Message----- From: Rudolph Pienaar [mailto:rudolph@nmr.mgh.harvard.edu] Sent: 25 August 2009 16:01 To: Ahmed, F, Me fahmed@sun.ac.za Cc: Nick Schmansky; Freesurfer Mailing List Subject: Re: [Freesurfer] installing on ubuntu
Hi Fatima --
Ahmed, F, Me fahmed@sun.ac.za wrote:
cd /usr/local tar xzvf freesurfer-Linux-<platform>-<release>-full.tar.gz
and I got the following error:
tar: freesurfer-Linux-centos4-stable-pub-v4.3.1-full.tar: Cannot
open: No such file or directory
That error in fact does make sense. The 'tar' command is trying to unpack the archive, but it is saying that it can't find the archive file. That most likely is because the archive file is *not* in the /usr/local folder (or directory).
I'm guessing that you downloaded the archive to your Desktop -- this is usually the case if you use 'firefox' to download. Assuming that to be the case, the *full* path to the archive is:
/home/fatima/Desktop/freesurfer-Linux-centos4-stable-pub-v4.3.1-full.tar
(assuming that your user name on your computer is 'fatima'). Sometimes 'firefox' might download to your 'Downloads' folder:
/home/fatima/Downloads/freesurfer-Linux-centos4-stable-pub-v4.3.1-full.tar
I'm going to assume the archive is on your Desktop since this is the most common. Now, in order to install, you need to make sure about two things:
1. That you properly specify the archive. 2. That you have permissions to unpack the archive.
When you login, you have permission to read/write files and folders only in your "home" folder, i.e. /home/fatima -- anywhere "outside" this, and you will probably need administrator permission. This administrator is typically called 'root' on Linux/Mac/Unix systems.
On a CentOS box, when you want to install, you should change your user to 'root'. This means typing:
$>su
The prompt will ask you for a password. This is the 'root' password and was setup by whomever setup your computer. This password is probably not the same as your, i.e. 'fatima', password. When you have done that, you will notice that the prompt has changed slightly:
#>
i.e., the '$' is now '#', signifying that you are now 'root'.
Now, assuming that the freesurfer archive is still in your (i.e. 'fatima's) Desktop, you should try:
$>su Password: <type root password> #>cd /usr/local #>tar xzvf /home/fatima/Desktop/freesurfer-Linux-centos4-stable-pub-v4.3.1-full.tar
and you should hopefully be all set. By the way, you don't need to type every single character in the name. Just type the first one or two and then press <tab>. The shell will fill in the rest as far as it can. So when you start typing '/home/fa' press <tab> and it will automatically fill out '/home/fatima'. Then continue typing '/Des' and press <tab> -- you will see '/home/fatima/Desktop'. Now continue and type '/free' and press <tab> then the whole 'freesurfer-Linux-centos4-stable-pub-v4.3.1-full.tar' will automatically be completed.
On Ubuntu, it's pretty much the same as CentOS, but we use 'sudo' instead of 'su', and you can use your password and not the 'root' password:
$>sudo bash Password: <type YOUR password> #>cd /usr/local #>tar xzvf /home/fatima/Desktop/freesurfer-Linux-centos4-stable-pub-v4.3.1-full.tar
in both cases, when you're done unpacking, simply type: 'exit' so that you are no longer the 'root' user and return to being 'fatima'.
HTH -=R
freesurfer@nmr.mgh.harvard.edu
-
Ahmed, F, Me <fahmed＠sun.ac.za> -
Feuerstein Philippe -
Matt Glasser -
Nick Schmansky -
Rudolph Pienaar