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| === Freesurfer install on Ubuntu Linux in WSL === | === Freesurfer on Ubuntu Linux in WSL === |
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| ... setup the FREESURFER_HOME environment variable. The 2nd command adds the environment variable settings into your bash shell init file, i.e., .bashrc ... developer@DESKTOP-LD48TB7:~$ '''export FREESURFER_HOME=/usr/local/freesurfer/7.4.1''' <<BR>> developer@DESKTOP-LD48TB7:~$ '''echo "export FREESURFER_HOME=/usr/local/freesurfer/7.4.1" >> $HOME/.bashrc''' <<BR>> ... check the Freesurfer release was installed under /usr/local/freesurfer/7.4.1 ... <<BR>> developer@DESKTOP-LD48TB7:~$ '''ls $FREESURFER_HOME''' <<BR>> {{attachment:ls_output.png}} <<BR>> '''If you have an existing licence.txt file from a previous freesurfer registration, you can copy it in to your home directory in Linux. Otherwise, you need to register an email address and download a license file you can receive at that email destination in order to run freesurfer commands. Fill out the form [[https://surfer.nmr.mgh.harvard.edu/registration.html|freesurfer registration]] and wait for the license.txt file to be emailed to you. ''' |
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| '''''... the development stream package is installed under /usr/local/freesurfer/7-dev. The 7.2.0 release install would be under /usr/local/freesurfer/7.2.0 There is no conflict with having multiple versions of freesufer installed under parallel subdirectories - you only need to change the setting of the FREESURFER_HOME environment variable ...''''' |
... go to your home directory ... |
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| <<BR>>developer@DESKTOP-LD48TB7:~$ '''ls /usr/local/freesurfer/7-dev/''' <<BR>>ASegStatsLUT.txt FreeSurferEnv.sh Simple_surface_labels2009.txt build-stamp.txt fsafd mni sources.csh tktools <<BR>>DefectLUT.txt SegmentNoLUT.txt WMParcStatsLUT.txt diffusion fsfast models sources.sh trctrain <<BR>>FreeSurferColorLUT.txt SetUpFreeSurfer.csh average docs lib python subjects <<BR>>FreeSurferEnv.csh SetUpFreeSurfer.sh bin etc matlab sessions tkmeditParcColorsCMA |
developer@DESKTOP-LD48TB7:~$ '''cd''' <<BR>> |
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| '''''... setup your shell with the necessary environment variables for X-windows graphics and freesurfer. You can add these directly to your shell init file, e.g., the .bashrc file for bash shell. You will also need a license file for freesurfer which can be pointed to by an environment variable ...''''' | ... then download and/or copy in your license.txt file and verify you can see it with the ls command ... |
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| <<BR>>developer@DESKTOP-LD48TB7:~$ '''echo "export XDG_RUNTIME_DIR=$HOME/.xdg" >> $HOME/.bashrc''' <<BR>>developer@DESKTOP-LD48TB7:~$ '''echo "export DISPLAY=:0" >> $HOME/.bashrc''' <<BR>>developer@DESKTOP-LD48TB7:~$ '''echo "export FREESURFER_HOME=/usr/local/freesurfer/7-dev" >> $HOME/.bashrc''' |
developer@DESKTOP-LD48TB7:~$ '''ls license.txt''' <<BR>> license.txt |
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| '''''... Add your license file and set FS_LICENSE to point to it ...''''' | ... set the environment variable FS_LICENSE to point to license.txt ... |
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| <<BR>>developer@DESKTOP-LD48TB7:~$ '''echo "export FS_LICENSE=$HOME/license.txt" >> $HOME/.bashrc''' <<BR>>developer@DESKTOP-LD48TB7:~$ '''echo "source /usr/local/freesurfer/7-dev/SetUpFreeSurfer.sh" >> $HOME/.bashrc''' |
<<BR>> developer@DESKTOP-LD48TB7:~$ '''echo "export FS_LICENSE=$HOME/license.txt" >> $HOME/.bashrc''' |
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| '''''... logout and log back in and verify you see the following ...''''' | ... set these environment variables for your display ... |
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| <<BR>>- - - - - - - -freesurfer-linux-ubuntu18_x86_64-dev-20210518-60f02e6- - - - - - - - | <<BR>> developer@DESKTOP-LD48TB7:~$ '''echo "export XDG_RUNTIME_DIR=$HOME/.xdg" >> $HOME/.bashrc''' <<BR>> developer@DESKTOP-LD48TB7:~$ '''echo "export DISPLAY=:0" >> $HOME/.bashrc''' ... set the Freesurfer environment to be setup when you open a new Linux terminal window ... <<BR>> developer@DESKTOP-LD48TB7:~$ '''echo "source $FREESURFER_HOME/SetUpFreeSurfer.sh" >> $HOME/.bashrc''' <<BR>> '''Open a new Ubuntu linux terminal window and verify you see the following output showing the Freesurfer environment has been set. Or you could just logout and log back in to Ubuntu Linux. If you do not see the output below in the new terminal window, then something went wrong with your environment variable settings above and/or the install of Freesurfer. You should stop and ask for help if the output is missing.''' <<BR>>- - - - - - - -freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460- - - - - - - - |
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| <<BR>>FREESURFER_HOME /usr/local/freesurfer/7-dev/ <<BR>>FSFAST_HOME /usr/local/freesurfer/7-dev//fsfast |
<<BR>>FREESURFER_HOME /usr/local/freesurfer/7.4.1/ <<BR>>FSFAST_HOME /usr/local/freesurfer/7.4.1//fsfast |
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| <<BR>>SUBJECTS_DIR /usr/local/freesurfer/7-dev//subjects | <<BR>>SUBJECTS_DIR /usr/local/freesurfer/7.4.1//subjects |
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| <<BR>>MNI_DIR /usr/local/freesurfer/7-dev//mni | <<BR>>MNI_DIR /usr/local/freesurfer/7.4.1//mni |
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| '''''... you should now be able to run freeview and other commands from the distribution pointed to by $FREESURFER_HOME/bin. Please note that if you see the following error when trying to run freeview ...''''' |
<<BR>> '''If you plan to run image viewing programs such as Freeview in LInux running under WSL, the next step is to setup an X-server running on the Windows host. Some notes are provided below for setting up Xming. Some users have found Moba Xterm to be a good choice.''' <<BR>> |
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| <<BR>>developer@DESKTOP-LD48TB7:~$ freeview <<BR>>QXcbConnection: Could not connect to display :0 <<BR>>Could not connect to any X display. |
[[https://surfer.nmr.mgh.harvard.edu/fswiki/FSL_wsl_xming|Xming and setup notes]] <<BR>> [[https://mobaxterm.mobatek.net|MobaXterm]] <<BR>> [[https://sourceforge.net/projects/vcxsrv|VcxSrv]] <<BR>> |
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| '''''... then modify your DISPLAY variable to contain your IP address before the :0 ...''''' | ... Once the X-server is running on the Windows host, you should be able to start running freeview commands ... |
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| <<BR>>developer@DESKTOP-LD48TB7:~$ grep nameserver /etc/resolv.conf <<BR>>nameserver 154.132.1.1 <<BR>>developer@DESKTOP-LD48TB7:~$ export DISPLAY="154.132.1.1:0" |
... if you see the following error when trying to run freeview ... |
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| '''''... edit the Xming X0.hosts file from the windows side to contain your IP address BELOW the entry for localhost ...''''' | <<BR>> developer@DESKTOP-LD48TB7:~$ '''freeview''' <<BR>> QXcbConnection: Could not connect to display :0 <<BR>> Could not connect to any X display. ... then try modifying your DISPLAY variable to contain your IP address before the :0 ... <<BR>> developer@DESKTOP-LD48TB7:~$ '''grep nameserver /etc/resolv.conf''' <<BR>> nameserver 154.132.1.1 <<BR>> developer@DESKTOP-LD48TB7:~$ '''export DISPLAY="154.132.1.1:0"''' ... if you have installed and setup Xming as your X-server on the windows host, then edit the Xming X0.hosts file to contain your machines IP address below the entry for localhost ... |
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| '''''... before edit ...''''' <<BR>>developer@DESKTOP-LD48TB7:~$ cat /mnt/c/"Program Files (x86)"/Xming/X0.hosts |
... before edit ... <<BR>>developer@DESKTOP-LD48TB7:~$ '''cat /mnt/c/"Program Files (x86)"/Xming/X0.hosts''' |
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| <<BR>>'''''... after edit ...''''' <<BR>>developer@DESKTOP-LD48TB7:~$ cat /mnt/c/"Program Files (x86)"/Xming/X0.hosts |
<<BR>>... after edit ... <<BR>>developer@DESKTOP-LD48TB7:~$ '''cat /mnt/c/"Program Files (x86)"/Xming/X0.hosts''' |
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| <<BR>>'''''... check DISPLAY matches IP address...''''' <<BR>>developer@DESKTOP-LD48TB7:~$ echo $DISPLAY |
<<BR>>... check DISPLAY matches IP address... <<BR>>developer@DESKTOP-LD48TB7:~$ '''echo $DISPLAY''' |
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| '''''... try running freeview again ...''''' | ... try running freeview again ... |
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| <<BR>>developer@DESKTOP-LD48TB7:~$ freeview | <<BR>>developer@DESKTOP-LD48TB7:~$ '''freeview''' |
Freesurfer on Ubuntu Linux in WSL
Please read the latest MS documentation about how to setup WSL (version2 as of this writing) on your Windows machine, MS WSL Dcoumentation. Once you are able to bring up a terminal window in WSL's pre-installed version of Ubuntu linux you can proceed to setting up the Freesurfer environment. As of this writing, WSL should install Ubuntu 22 Linux and so the install of a Freesurfer Ubuntu 22 package is listed below.
The commands below shows how to download and install the freesurfer package. That is followed by notes on setting up a 3rd party X-windows server on the host Windows machine using Xming. If you do not need to view any brain images, e.g., through Freeview, then there is no need to setup the X-Windows server.
We do not advise manually trying to install packages in the Ubuntu Linux image in order to get freesurfer to run. Please allow the installer to try and determine what packages are needed on the system and install them.
developer@DESKTOP-LD48TB7:~$ cd
developer@DESKTOP-LD48TB7:~$ wget https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer_ubuntu22-7.4.1_amd64.deb
... download output ...
developer@DESKTOP-LD48TB7:~$ ls freesurfer_ubuntu22-7.4.1_amd64.deb
freesurfer_ubuntu22-7.4.1_amd64.deb
... update the package information in Ubuntu linux ...
developer@DESKTOP-LD48TB7:~$ sudo apt-get update -y
[sudo] password for developer:
... output from package updates ...
... install the freesurfer distribution under /usr/local/freesurfer/<release>. Anwer "Y" to any prompts ...
developer@DESKTOP-LD48TB7:~$ sudo apt-get -y install ./freesurfer_ubuntu22-7.4.1_amd64.deb
[sudo] password for developer:
The following NEW packages will be installed:
... output from package updates followed by install of freesurfer package ...
... setup the FREESURFER_HOME environment variable. The 2nd command adds the environment variable settings into your bash shell init file, i.e., .bashrc ...
developer@DESKTOP-LD48TB7:~$ export FREESURFER_HOME=/usr/local/freesurfer/7.4.1
developer@DESKTOP-LD48TB7:~$ echo "export FREESURFER_HOME=/usr/local/freesurfer/7.4.1" >> $HOME/.bashrc
... check the Freesurfer release was installed under /usr/local/freesurfer/7.4.1 ...
developer@DESKTOP-LD48TB7:~$ ls $FREESURFER_HOME
If you have an existing licence.txt file from a previous freesurfer registration, you can copy it in to your home directory in Linux. Otherwise, you need to register an email address and download a license file you can receive at that email destination in order to run freesurfer commands. Fill out the form freesurfer registration and wait for the license.txt file to be emailed to you.
... go to your home directory ...
developer@DESKTOP-LD48TB7:~$ cd
... then download and/or copy in your license.txt file and verify you can see it with the ls command ...
developer@DESKTOP-LD48TB7:~$ ls license.txt
license.txt
... set the environment variable FS_LICENSE to point to license.txt ...
developer@DESKTOP-LD48TB7:~$ echo "export FS_LICENSE=$HOME/license.txt" >> $HOME/.bashrc
... set these environment variables for your display ...
developer@DESKTOP-LD48TB7:~$ echo "export XDG_RUNTIME_DIR=$HOME/.xdg" >> $HOME/.bashrc
developer@DESKTOP-LD48TB7:~$ echo "export DISPLAY=:0" >> $HOME/.bashrc
... set the Freesurfer environment to be setup when you open a new Linux terminal window ...
developer@DESKTOP-LD48TB7:~$ echo "source $FREESURFER_HOME/SetUpFreeSurfer.sh" >> $HOME/.bashrc
Open a new Ubuntu linux terminal window and verify you see the following output showing the Freesurfer environment has been set. Or you could just logout and log back in to Ubuntu Linux. If you do not see the output below in the new terminal window, then something went wrong with your environment variable settings above and/or the install of Freesurfer. You should stop and ask for help if the output is missing.
- - - - - - - -freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460- - - - - - - -
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer/7.4.1/
FSFAST_HOME /usr/local/freesurfer/7.4.1//fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /usr/local/freesurfer/7.4.1//subjects
INFO: /home/developer/matlab/startup.m does not exist ... creating
MNI_DIR /usr/local/freesurfer/7.4.1//mni
If you plan to run image viewing programs such as Freeview in LInux running under WSL, the next step is to setup an X-server running on the Windows host. Some notes are provided below for setting up Xming. Some users have found Moba Xterm to be a good choice.
Xming and setup notes
MobaXterm
VcxSrv
... Once the X-server is running on the Windows host, you should be able to start running freeview commands ...
... if you see the following error when trying to run freeview ...
developer@DESKTOP-LD48TB7:~$ freeview
QXcbConnection: Could not connect to display :0
Could not connect to any X display.
... then try modifying your DISPLAY variable to contain your IP address before the :0 ...
developer@DESKTOP-LD48TB7:~$ grep nameserver /etc/resolv.conf
nameserver 154.132.1.1
developer@DESKTOP-LD48TB7:~$ export DISPLAY="154.132.1.1:0"
... if you have installed and setup Xming as your X-server on the windows host, then edit the Xming X0.hosts file to contain your machines IP address below the entry for localhost ...
... before edit ...
developer@DESKTOP-LD48TB7:~$ cat /mnt/c/"Program Files (x86)"/Xming/X0.hosts
localhost
... after edit ...
developer@DESKTOP-LD48TB7:~$ cat /mnt/c/"Program Files (x86)"/Xming/X0.hosts
localhost
154.132.1.1
... check DISPLAY matches IP address...
developer@DESKTOP-LD48TB7:~$ echo $DISPLAY
154.132.1.1:0
... try running freeview again ...
developer@DESKTOP-LD48TB7:~$ freeview