3 NeuroDebian Virtual Machine
4 ===========================
10 For those who are not yet running a Debian-based operation system we offer a
11 `virtual machine`_ that can be used with `VirtualBox`_, allowing users to benefit
12 from a Debian-based research environment on other operating systems.
13 This virtual machine initially comes as a compact Debian installation that can,
14 once installed, be equipped with a large variety of neuroscience software with
15 just a few mouse clicks (e.g. AFNI_, Caret_, FSL_, PyMVPA_).
17 .. _virtual machine: http://en.wikipedia.org/wiki/Virtual_machine
18 .. _AFNI: http://afni.nimh.nih.gov/afni/
19 .. _Caret: http://brainvis.wustl.edu/wiki/index.php/Caret:About
20 .. _FSL: http://www.fmrib.ox.ac.uk/fsl/
21 .. _PyMVPA: http://www.pymvpa.org
27 * `NeuroDebian 6.0.4 image (32bit)
28 <http://neuro.debian.net/debian/vm/NeuroDebian_6.0.4_i386.ova>`_ [~558MB]
30 *This image should work on virtually all systems that are supported by*
31 VirtualBox_ *and can be used whenever the, otherwise preferable, 64bit image
32 is not compatible with a host machine.*
34 * `NeuroDebian 6.0.4 image (64bit)
35 <http://neuro.debian.net/debian/vm/NeuroDebian_6.0.4_amd64.ova>`_ [~573MB]
37 *This image only works on 64bit host machines with active hardware
38 virtualization support. The should include all recent Apple hardware and most
39 64bit Windows systems.*
41 Virtual appliances above carry guest additions for 4.x series of the
42 VirtualBox. If you still have VirtualBox 3.x, use previous 6.0.2
45 * `NeuroDebian 6.0.2 image (32bit)
46 <http://neuro.debian.net/debian/vm/neurodebian_6.0.2_i386.zip>`_ [~545MB]
48 * `NeuroDebian 6.0.2 image (64bit)
49 <http://neuro.debian.net/debian/vm/neurodebian_6.0.2_amd64.zip>`_ [~560MB]
53 You can verify that you have downloaded archives correctly using
55 <http://neuro.debian.net/debian/vm/MD5SUMS>`_ . You can also verify
56 the authenticity of the `MD5SUMS
57 <http://neuro.debian.net/debian/vm/MD5SUMS>`_ itself using `gpg
59 <http://neuro.debian.net/debian/vm/MD5SUMS.gpg>`_ signed with
60 NeuroDebian archive key.
62 * `VirtualBox download page <http://www.virtualbox.org/wiki/Downloads>`_ (Windows, Linux, Mac,
65 *This webpage offers installers of the VirtualBox application, as well as the
73 * Updated shipped virtualbox-ose guest-utils and guest-x11 to 4.0.4
75 6.0.3 -- 12 Jun 2011 [Superseded in the archive by 6.0.4]
77 * Updated to Squeeze 6.0.1
78 * Updated VirtualBox guest additions to 4.0.4 from backports.debian.org
79 * Appliance is available as a single file (.ova) ready for the import
88 The virtual machine contains an installation of `Debian 6.0 (squeeze)`_ with a
89 GNOME_ desktop environment. All installed software comes from standard Debian
90 packages, or prospective Debian packages from NeuroDebian. This means that all
91 contained software is readily available for any system running a Debian
92 operating system (or a recent Ubuntu release). The virtual machine can be seen
93 as a showcase of what Debian for neuroscience research feels like. Moreover,
94 once downloaded this virtual machine can be kept up to date, just as any other
95 Debian installation. Using convenient graphical package management tools users
96 will benefit from security bug fixes provided by the Debian project for the
97 whole operating system, as well as from software updates for
98 neuroscience-related packages.
100 .. _Debian 6.0 (squeeze): http://www.debian.org/releases/squeeze
101 .. _GNOME: http://www.gnome.org/
107 The following video shows how to get the NeuroDebian virtual machine running
108 on your machine. The installation is shown for Mac OS X. It should, however, be
109 very similar on a Windows box. If you cannot watch the video, please take a
110 look at the written instructions below.
114 <iframe title="YouTube video player"
115 class="youtube-player"
119 src="http://www.youtube.com/embed/eqfjKV5XaTE?hd=1"
120 frameborder="0"></iframe>
122 First download and install a recent version of VirtualBox_. VirtualBox is a
123 virtualization software that is freely available for Windows, MacOS X, Solaris,
124 and Linux. VirtualBox comes with a comprehensive manual that should answer
125 potential questions regarding installation and maintenance.
127 .. _VirtualBox: http://www.virtualbox.org
129 Next, download the most recent version of the NeuroDebian virtual machine from
130 the Downloads_ section. The machine is distributed as a zip file. Please
131 extract this file, using appropriate software for your operating system.
132 Once extracted, start VirtualBox and select "Import Appliance" from the file
135 .. image:: pics/vm_import_app.jpg
137 The next dialog will ask you to choose a virtual machine. Please navigate to the
138 extracted NeuroDebian download and select the `.ovf` file.
140 .. image:: pics/vm_import_wizard.jpg
142 You can finish importing of NeuroDebian by clicking on *next* a couple of
143 times. There is no need to change anything, as we will get through the
144 settings in a second. Importing of the virtual machine will take a short
145 while, as it is distributed in a compressed format that now gets extracted
146 (total extracted size about 2 GB). Once imported, the NeuroDebian virtual
147 machine will appear in the list of available machines. Do **not** start it yet,
148 but select NeuroDebian and hit the *Settings* button. In the following dialog
149 you'll have a chance to configure the machine. You can assign the amount of RAM
150 that should be made available to it (for serious fMRI data processing, please
151 allow at least 2 GB). If you have a recent computer with multiple CPU cores,
152 you can also decide how many cores should be used by the virtual machine. If
153 you have a large screen you should increase the display memory to 32 MB in the
156 .. image:: pics/vm_add_host_folder.jpg
158 However, most important is the *Shared Folders* setup. Shared folders allow the
159 virtual machine to access the local harddrive of the host computer. This is an
160 easy way to access data on the computer without duplicating it or using the
161 network to access it. The virtual machine is preconfigured to access a shared
162 folder named labeled "host". Click on the *add* button to select a folder that
163 shall be accessible by the machine (e.g. your home directory) and put "host" as
164 the folder name. Note, the folder name is simply a label. Your directory will
167 .. image:: pics/vm_host_folder.jpg
169 Finally, close the settings dialog. You have now completed the setup, and you
170 can start the virtual machine by hitting the *Start* button. A new window will
171 appear showing the boot process. After a short while the NeuroDebian desktop
172 will appear, and a setup wizard will guide your through the final steps of the
173 configuration. You can now explore the system. The virtual machine is connected
174 with your host computer, and shares its Internet connection. Via this
175 connection you can update the contained software packages at any time.
177 .. image:: pics/vm_settings.jpg
179 The virtual machine logs yourself in automatically. The name of the virtual
180 machine user is `brain` and the password is `neurodebian`. The *root* password
181 is also `neurodebian`. In most cases, however, you should not be forced to type
182 the password, since `sudo` is configured to work without it.
186 For increased security you might want to change the default password. You can
187 do so by opening a terminal window and running the ``passwd`` command.
190 Working with the virtual machine
191 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
193 The next video is a demonstration of some basic desktop integration features.
194 It shows how to use the virtual machine in full-screen and seamless mode, shared
195 folder access, software installation, as well as suspending and resuming the
200 <iframe title="YouTube video player"
201 class="youtube-player"
205 src="http://www.youtube.com/embed/OV7fYSEoOeQ?hd=1"
206 frameborder="0"></iframe>
209 .. _chap_vm_troubleshooting:
214 Updating the VM or installing new packages doesn't work.
216 The VM uses as service that tries to figure out the best/closest package
217 repository for you. In some network environments this service might not work
218 well, or not at all. To check if this is a problem, you can modify the
219 respective configuration by hand. Edit ``/etc/apt/sources.list`` (you need to
220 use ``sudo`` for that) and replace the package repository URL with a mirror
221 close to you. A comprehensive list of mirrors is available at:
222 http://www.debian.org/mirror/list
224 Pick one and replace all ``geomirror.debian.net`` URLs with the new mirror
225 URL. For example, in Canada you might want to change::
227 deb http://i386-geomirror.debian.net/debian squeeze main non-free contrib
231 deb http://ftp.ca.debian.org/debian/ squeeze main non-free contrib
233 Only modify lines that refer to ``geomirror`` (all of them), but do **not**
234 modify entries for ``security.debian.org``.
236 I cannot hear sounds played in the virtual machine.
238 By default the sound is muted. To enable playback launch the mixer applet by
239 clicking on the mixer icon in the task bar. Unmute the master volume control.
240 Now click on the "Volume control" to load the channel mixer dialog. Unmute
241 the "Master" and "PCM" channels and raise the volume as desired. You should
242 now be able to hear sounds played within the virtual machines through your
243 host computer's speakers.
245 I have upgraded VirtualBox from 3.x series to 4.x, and my VM lost
246 mounted host directories.
248 NeuroDebian VMs prior 6.0.3 were shipped with guest additions from
249 3.x series of VirtualBox and some initial versions of VirtualBox in
250 4.x series have failed to mount host directories properly.
251 VirtualBox 4.0.8 seems to work fine with guest additions from 3.x
252 series. If you nevertheless want to upgrade guest additions within
253 NeuroDebian VM, please rebuild the version available from the
256 sudo apt-get install -y linux-headers-2.6-amd64 # or -686 for 32bit
257 sudo apt-get install -y -t squeeze-backports virtualbox-ose-guest-kdms \
258 virtualbox-ose-guest-utils virtualbox-ose-guest-x11