NeuroDebian Virtual Machine

Installation | Working with the virtual machine | Troubleshooting | What has changed

[...] NeuroDebian allows both researchers and the public to easily replicate the entire experimental procedure, a feature rendered difficult or often impossible by proprietary software packages that most scientists rely on nowadays. I have been increasingly using NeuroDebian in a Virtual Machine because Linux operating systems are not supported by the university. [...] Moreover, powered by NeuroDebian’s openness, I see a reason to publish the full code of our experimental and analysis scripts. [NeuroDebian] makes the goal of open science finally viable.

—– Jonas Kubilius [2011-06-18] Ph.D. student, Laboratories of Biological and Experimental Psychology, K. U. Leuven, Belgium

For all systems running a non-Debian-based operation system, such as MS Windows or Mac OS X, we offer a virtual machine that can be equipped with a large variety of neuroscience software with just a few mouse clicks (e.g. AFNI, FSL, PyMVPA).

The virtual machine contains an installation of Debian 7.0 (wheezy) with a XFCE4 desktop environment. All installed software comes from standard Debian packages, or prospective Debian packages from NeuroDebian. The virtual machine can be seen as a showcase of what Debian for neuroscience research feels like. Once downloaded this virtual machine can be kept up to date, just as any other Debian installation. Using convenient graphical package management tools users will benefit from security bug fixes provided by the Debian project for the whole operating system, as well as from software updates for neuroscience-related packages.

Even on Debian-based systems this virtual machine is an excellent way to maintain an analysis environment that remains identical throughout the lifetime of a study and that can be archived alongside acquired data and publications. This is a much more practical way than freezing the entire software stack of a whole workstation, where it quickly becomes troublesome to combine the desire for latest research methodology for new studies and the need for stability for ongoing projects.

Installation

The following instructions demonstrate how to install the NeuroDebian virtual machine – here shown exemplary for Mac OS X, but the procedure is virtually identical on a Windows box. There is also a video tutorial at coffee break length. [Virtual machine setup video tutorial].

If you don’t have t already, first download and install a recent version of VirtualBox. VirtualBox is a virtualization software that is freely available for Windows, MacOS X, Solaris, and Linux. VirtualBox comes with a comprehensive manual that should answer potential questions regarding installation and maintenance.

Obtain the most recent version of the NeuroDebian virtual machine by visiting http://neuro.debian.net and selecting your operating system and a download server on the frontpage.

Start VirtualBox and select “Import Appliance” from the file menu.

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The next dialog will ask you to choose a virtual machine. Please navigate to the extracted NeuroDebian download and select the .ova (or extracted .ovf for older appliances shipped as .zip) file.

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You can finish importing of NeuroDebian by clicking on next a couple of times. There is no need to change anything, as we will get through the settings in a second. Importing of the virtual machine will take a short while, as it is distributed in a compressed format that now gets extracted (total extracted size about 2 GB). Once imported, the NeuroDebian virtual machine will appear in the list of available machines. Do not start it yet, but select NeuroDebian and hit the Settings button. In the following dialog you’ll have a chance to configure the machine. You can assign the amount of RAM that should be made available to it (for serious fMRI data processing, please allow at least 2 GB). If you have a recent computer with multiple CPU cores, you can also decide how many cores should be used by the virtual machine.

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However, most important is the Shared Folders setup. Shared folders allow the virtual machine to access the local harddrive of the host computer. This is an easy way to access data on the computer without duplicating it or using the network to access it. The virtual machine is preconfigured to access a shared folder named labeled “host”. Click on the add button to select a folder that shall be accessible by the machine (e.g. your home directory) and put “host” as the folder name and mark it to be auto-mounted. Note, the folder name is simply a label. Your directory will not be renamed.

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If you have a large screen you should increase the display memory to 32 MB in the Display settings. Also you might like to enable the support for 3D Acceleration

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Finally, close the settings dialog. You have now completed the setup, and you can start the virtual machine by hitting the Start button. A new window will appear showing the boot process. After a short while the NeuroDebian desktop will appear, and a setup wizard will guide your through the final steps of the configuration. You can now explore the system. The virtual machine is connected with your host computer, and shares its Internet connection. Via this connection you can update the contained software packages at any time.

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The virtual machine logs yourself in automatically. This is the default account:

user:brain
password:neurodebian
root password:neurodebian

In most cases you should not be forced to type the password, because sudo is configured to work without it.

Note

For increased security you might want to change the default password. You can do so by opening a terminal window and running the passwd command.

Working with the virtual machine

The NeuroDebian virtual machine has very low maintenance demands. We have prepared a short video demo that shows most typical procedures that you will probably perform while working with NeuroDebian inside a virtual machine: use the virtual machine in full-screen and seamless mode, shared folder access, software installation, as well as suspending and resuming the virtual machine. [Virtual machine handling video tutorial]

Troubleshooting

Click on an item to expand it
Updating the VM or installing new packages doesn’t work

The VM uses as service that tries to figure out the best/closest package repository for you. In some network environments this service might not work well, or not at all. To check if this is a problem, you can modify the respective configuration by hand. Edit /etc/apt/sources.list (you need to use sudo for that) and replace the package repository URL with a mirror close to you. A comprehensive list of mirrors is available at: http://www.debian.org/mirror/list

Pick one and replace all geomirror.debian.net URLs with the new mirror URL. For example, in Canada you might want to change:

deb http://i386-geomirror.debian.net/debian squeeze main non-free contrib

to:

deb http://ftp.ca.debian.org/debian/ squeeze main non-free contrib

Only modify lines that refer to geomirror (all of them), but do not modify entries for security.debian.org.

Our proxy setup at work prevents APT from downloading packages

APT needs to be told how to access the proxy. Talk to your local sysadmin and ask for the proxy’s address (maybe a username and password too), as well as the ports for HTTP and FTP proxies. With this information add the following lines in the file, /etc/apt/apt.conf.d/80proxy. This will ensure that after an upgrade changes won’t be lost:

Acquire::http::proxy "http://<username>:<password>@<proxy>:<port>/";
Acquire::ftp::proxy "ftp://<username>:<password>@<proxy>:<port>/";
Acquire::https::proxy "https://<username>:<password>@<proxy>:<port>/";
I cannot hear sounds played in the virtual machine
By default the sound is muted. To enable playback launch the mixer applet by clicking on the mixer icon in the task bar. Unmute the master volume control. Now click on the “Volume control” to load the channel mixer dialog. Unmute the “Master” and “PCM” channels and raise the volume as desired. You should now be able to hear sounds played within the virtual machines through your host computer’s speakers.
My VM lost mounted host directories after upgrading from VirtualBox from 3.x to 4.x

NeuroDebian VMs prior 6.0.3 were shipped with guest additions from 3.x series of VirtualBox and some initial versions of VirtualBox in 4.x series have failed to mount host directories properly. VirtualBox 4.0.8 seems to work fine with guest additions from 3.x series. If you nevertheless want to upgrade guest additions within NeuroDebian VM, please rebuild the version available from the backports:

sudo apt-get install -y linux-headers-2.6-amd64 # or -686 for 32bit
sudo apt-get install -y -t squeeze-backports virtualbox-ose-guest-dkms \
     virtualbox-ose-guest-utils  virtualbox-ose-guest-x11

and reboot VM.

I am still running an older VirtualBox 3.x

Download one of the image files listed below. These older releases are distributed as a zip file. Please extract all files from the .zip file, using appropriate software for your operating system.

What has changed

Click on an item to expand it
7.4.20140423 – 24 Apr 2014
7.4.0 – 28 Feb 2014
  • VM appliance based on the official wheezy point release 7.4.
7.2.0 – 03 Nov 2013
  • VM appliance based on the official wheezy point release 7.2.

  • Ships with updated neurodebian-* packages: - installs ipython notebook and qtconsole for “Scientific Python”

    and “PyMVPA tutorial” welcome wizard choices.

7.0.0 – 15 May 2013
  • VM appliance based on the official wheezy release.
  • Uses xfce4-terminal by default (instead of urxvt/rxvt-unicode as in beta-releases)
6.999.b4.20130421 – 22 Apr 2013
  • Refreshed VM appliance to avoid lengthy initial upgrade
6.999.b4.20121231 – 31 Dec 2012
6.0.6 – 01 Oct 2012
  • Updated core system to Debian squeeze 6.0.6
6.0.5 – 10 Nov 2011
  • Updated core system to Debian squeeze 6.0.3
  • Updated shipped virtualbox-ose guest-utils and guest-x11 to 4.0.10
    • ~/host is now symlinked to correct path /media/sf_host
    • brain user is added to vboxsf group so mounted host directories should become readily available
  • Root partition size and swap space got doubled in size (40GB and 2GB correspondingly). Space is allocated dynamically so the actual size of the virtual drive should not grow unless you use it
6.0.4 – 13 Jun 2011
  • Updated shipped virtualbox-ose guest-utils and guest-x11 to 4.0.4
6.0.3 – 12 Jun 2011 [Superseded in the archive by 6.0.4]
  • Updated to Squeeze 6.0.1
  • Updated VirtualBox guest additions to 4.0.4 from backports.debian.org
  • Appliance is available as a single file (.ova) ready for the import
6.0.2 – 08 Feb 2011
  • Minor update
6.0.1 – 01 Dec 2010
  • Minor update

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