eXTReMe Tracker
Sep 122016
 

There is good news for those who use neuroimaging tools such as AFNI, FSL and FreeSurfer on their Windows machines. The limitation is that they can only be run on Windows 10 with anniversary update. Does it use a Virtual Machine? No. It runs “natively” on Windows 10, so you can save, print, resize or hide any interface just like a Windows program.

Freeview running in Windows 10

Freesurfer on Windows 10

Before I get into how to install FreeSurfer, I must thank the author at K-Lab for the post on “How to run FSL on Windows 10“. That post describes how to install BASH on Windows 10 in the first few steps. Sadly it is not available for Windows 7/8. It uses Ubuntu 14.04 LTS which will be supported by Canonical until 2019. We hope by then Windows would incorporate the Ubuntu 16.04 LTS as the default distribution.

I’ll repeat a few things (steps 1-5) that Lin4Neuro wrote on how to get BASH and X-server on Windows 10.

  1. Install Linux BASH shell on Windows 10:
    There is detailed tutorial with screenshots on how to do this at the following site.
    How to Install and Use the Linux Bash Shell on Windows 10
  2. Install the updates:
    Before adding any tools, you should first download and install the updates for Ubuntu. Run the following commands at the terminal

    sudo apt-get update
    sudo apt-get upgrade
  3. Install the X server:
    Installing BASH will allow you to run applications on a command line but in order to run any GUIs for neuroimaging tools you require a X-server for windows. The most popular software for this is Xming. You can download and install it with default settings.
    Xming X server for Windows
  4. Running X server:
    Run Xming by searching it from start menu. When it is loaded you should see this when you go to show hidden icons button at the bottom right corner of your desktop.
    xming_server
  5. In order for X server to work with BASH run the following command at the terminal
    echo "export DISPLAY=localhost:0.0" >> ~/.bashrc

    This will add the environment variable for display to the .bashrc file.


  6. Downloading Freesurfer:
    You can obtain your copy of Freesurfer from their web page. I would recommend getting the nightly build as I was having some trouble running the stable version v5.30, especially some of the graphical windows. If you want to try the stable version download the 64-bit centos6 stable v5.3.0 freesurfer. I would encourage getting the v6.0 nightly build even though it is not the official release. You can go back and reinstall the stable version 6.0 once it is released.To download your choice of FreeSurfer type this command at the terminal:
    For stable release v5.3.0

    ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz

    For nightly build

    wget ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-Linux-centos6_x86_64-dev.tar.gz

    Hint: You can copy the link with your mouse and when you right-click at the terminal, it will be automatically pasted so you don’t have to type it in manually.
    This is a large file (~4.6GB) so it may take some time to download it based on your network speed.

  7.  Extract the zipped file to install it. It is customary to install it at /usr/local/ so let’s extract it to that directory.
    sudo tar -xzf freesurfer-Linux-centos6_x86_64-dev.tar.gz -C /usr/local/

    You will require your admin password (for Linux) to extract it to /usr/local. Again this step can take few minutes since it is extracting a file that’s several gigabytes in size. Once extracted, we’ll have to change permissions on that folder.

    sudo chmod -R 755 /usr/local/freesurfer

    This allows you to make changes to files in that folder.

  8. Obtain the FreeSurfer license:
    In order to run the FreeSurfer applications you need to register and obtain a license from their website.
    FreeSurfer Registration
    Once you have the license emailed to you, copy the contents between the lines that read “cut here” and create a license.txt file.

    sudo nano /usr/local/freesurfer/license.txt

    fs_lic
    Paste the contents with right-click
    Press ctrl+X to exit
    Press y to accept and save it as license.txt
    Hit Enter

  9. Add FreeSurfer path to .bashrc:
    echo "export FREESURFER_HOME=/usr/local/freesurfer" >> ~/.bashrc
    echo "source $FREESURFER_HOME/SetUpFreeSurfer.sh" >> ~/.bashrc
  10. Dependencies: libjpeg.so.62
    Generally there is a libjpeg dependency that is required by FreeSurfer graphics. It doesn’t come with the basic Ubuntu installation but it can be installed using:

    sudo apt-get install libjpeg62
  11. Final check:
    Check that the Xming server is running and it says Xming Server:0.0 when you hover the mouse on the icon in the lower right hand corner.Type bash at the terminal. You should see the following:

    -------- freesurfer-Linux-centos6_x86_6.0 --------
    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
  12. Test your installation:
    Check if everything works by going through some of the examples listed on the FreeSurfer website.
    FreeSurfer examples
    If everything has been installed correctly you should be able to run command line functions and open GUIs just like on a Mac or Linux machine.
    tksurfer_win10If you have any questions about the installation, please post a comment. If you have questions about FreeSurfer please visit the FreeSurfer user community mail archives.
Jul 202012
 

In the newer versions of Linux, an open source driver is usually installed by default to run the graphic cards. However this driver can sometimes be absolutely messy, and it is essential to remove the Nouveau driver and install the binary driver from Nvidia.

However, if after you reboot into the service mode from grub menu, and try to install the NVIDIA-Linux-x86_64-xxx.run driver in the init 3 level, the program will kick you out saying that the Nouveau driver is still in use.

The way to disable the Nouveau drivers from kernel is to boot in the service mode and run the following commands:

echo options nouveau modeset=0 | sudo tee -a /etc/modprobe.d/nouveau-kms.conf
 update-initramfs -u

Once its done reconfiguring the kernel, you will need to reboot, and again get to service mode.

After that, get into init 3 mode, and install the NVIDIA-Linux-x86-64.xxx.run script. The installation should be successful at this point.

Sep 192011
 

The latest version of Ubuntu is heavily based upon Unity environment. Unfortunately Unity has no track record of playing nice with existing gnome programs. For network applications such as VNC, Unity crashes the program with whole bunch of errors. These crashes are observed occasionally in the Ubuntu 11.04 (Natty Narwhal) release, and most certainly in the latest beta 1 release of Ubuntu 11.10 (Oneiric Ocelot).

If you have gotten comfortable with Ubuntu and want to continue using Gnome as the main environment, you can do so by using Linux Mint 11 (Katya). It has the same repositories as Ubuntu and you can even use the ubuntu-restricted-extras and build-essential packages which lets you obtain some of the fonts, codecs and libraries that Ubuntu fetches for you.

Ubuntu is starting to put more emphasis on making their release into an eye-candy, at the cost of reduced functionality. Having used Ubuntu since Dapper Drake days, its sad to ditch it for another distro. IMO Ubuntu 10.04 was the cleanest distro they put out – things have been going downhill after that. Linux Mint on the other hand picked up at the point when Ubuntu started to go dysfunctional. It has everything that Ubuntu should have been. There isn’t much to write about Mint 11. Its very similar to Ubuntu 10.04, has a newer kernel 2.6.38.xx, clean graphics, and the same repositories as Ubuntu. The transition is very easy, and things look a lot more neater in Mint.

To recap: If you are currently using Ubuntu and are afraid to upgrade to the 11.10 release, your fear is quite justified. Make a backup of your /home folder and go for a clean install of Linux Mint instead. I moved to Mint about a month ago and have had a rather smooth sailing so far.