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 6.0.1 image (32bit)
28 <http://neuro.debian.net/debian/vm/neurodebian_6.0.1_i386.zip>`_ [~560MB]
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 6.0.1 image (64bit)
35 <http://neuro.debian.net/debian/vm/neurodebian_6.0.1_amd64.zip>`_ [~570MB]
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.*
43 You can verify that you have downloaded archives correctly using
45 <http://neuro.debian.net/debian/vm/MD5SUMS>`_ . You can also verify
46 the authenticity of the `MD5SUMS
47 <http://neuro.debian.net/debian/vm/MD5SUMS>`_ itself using `gpg
49 <http://neuro.debian.net/debian/vm/MD5SUMS.gpg>`_ signed with
50 NeuroDebian archive key.
52 * `VirtualBox download page <http://www.virtualbox.org/wiki/Downloads>`_ (Windows, Linux, Mac,
55 *This webpage offers installers of the VirtualBox application, as well as the
62 The virtual machine contains an installation of `Debian 6.0 (squeeze)`_ with a
63 GNOME_ desktop environment. All installed software comes from standard Debian
64 packages, or prospective Debian packages from NeuroDebian. This means that all
65 contained software is readily available for any system running a Debian
66 operating system (or a recent Ubuntu release). The virtual machine can be seen
67 as a showcase of what Debian for neuroscience research feels like. Moreover,
68 once downloaded this virtual machine can be kept up to date, just as any other
69 Debian installation. Using convenient graphical package management tools users
70 will benefit from security bug fixes provided by the Debian project for the
71 whole operating system, as well as from software updates for
72 neuroscience-related packages.
74 .. _Debian 6.0 (squeeze): http://www.debian.org/releases/squeeze
75 .. _GNOME: http://www.gnome.org/
81 The following video shows how to get the NeuroDebian virtual machine running
82 on your machine. The installation is shown for Mac OS X. It should, however, be
83 very similar on a Windows box. If you cannot watch the video, please take a
84 look at the written instructions below.
88 <iframe title="YouTube video player"
89 class="youtube-player"
93 src="http://www.youtube.com/embed/eqfjKV5XaTE?hd=1"
94 frameborder="0"></iframe>
96 First download and install a recent version of VirtualBox_. VirtualBox is a
97 virtualization software that is freely available for Windows, MacOS X, Solaris,
98 and Linux. VirtualBox comes with a comprehensive manual that should answer
99 potential questions regarding installation and maintenance.
101 .. _VirtualBox: http://www.virtualbox.org
103 Next, download the most recent version of the NeuroDebian virtual machine from
104 the Downloads_ section. The machine is distributed as a zip file. Please
105 extract this file, using appropriate software for your operating system.
106 Once extracted, start VirtualBox and select "Import Appliance" from the file
109 .. image:: pics/vm_import_app.jpg
111 The next dialog will ask you to choose a virtual machine. Please navigate to the
112 extracted NeuroDebian download and select the `.ovf` file.
114 .. image:: pics/vm_import_wizard.jpg
116 You can finish importing of NeuroDebian by clicking on *next* a couple of
117 times. There is no need to change anything, as we will get through the
118 settings in a second. Importing of the virtual machine will take a short
119 while, as it is distributed in a compressed format that now gets extracted
120 (total extracted size about 2 GB). Once imported, the NeuroDebian virtual
121 machine will appear in the list of available machines. Do **not** start it yet,
122 but select NeuroDebian and hit the *Settings* button. In the following dialog
123 you'll have a chance to configure the machine. You can assign the amount of RAM
124 that should be made available to it (for serious fMRI data processing, please
125 allow at least 2 GB). If you have a recent computer with multiple CPU cores,
126 you can also decide how many cores should be used by the virtual machine. If
127 you have a large screen you should increase the display memory to 32 MB in the
130 .. image:: pics/vm_add_host_folder.jpg
132 However, most important is the *Shared Folders* setup. Shared folders allow the
133 virtual machine to access the local harddrive of the host computer. This is an
134 easy way to access data on the computer without duplicating it or using the
135 network to access it. The virtual machine is preconfigured to access a shared
136 folder named labeled "host". Click on the *add* button to select a folder that
137 shall be accessible by the machine (e.g. your home directory) and put "host" as
138 the folder name. Note, the folder name is simply a label. Your directory will
141 .. image:: pics/vm_host_folder.jpg
143 Finally, close the settings dialog. You have now completed the setup, and you
144 can start the virtual machine by hitting the *Start* button. A new window will
145 appear showing the boot process. After a short while the NeuroDebian desktop
146 will appear, and a setup wizard will guide your through the final steps of the
147 configuration. You can now explore the system. The virtual machine is connected
148 with your host computer, and shares its Internet connection. Via this
149 connection you can update the contained software packages at any time.
151 .. image:: pics/vm_settings.jpg
153 The virtual machine logs yourself in automatically. The name of the virtual
154 machine user is `brain` and the password is `neurodebian`. The *root* password
155 is also `neurodebian`. In most cases, however, you should not be forced to type
156 the password, since `sudo` is configured to work without it.
160 For increased security you might want to change the default password. You can
161 do so by opening a terminal window and running the ``passwd`` command.
164 Working with the virtual machine
165 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
167 The next video is a demonstration of some basic desktop integration features.
168 It shows how to use the virtual machine in full-screen and seamless mode, shared
169 folder access, software installation, as well as suspending and resuming the
174 <iframe title="YouTube video player"
175 class="youtube-player"
179 src="http://www.youtube.com/embed/OV7fYSEoOeQ?hd=1"
180 frameborder="0"></iframe>
186 I cannot hear sounds played in the virtual machine.
188 By default the sound is muted. To enable playback launch the mixer applet by
189 clicking on the mixer icon in the task bar. Unmute the master volume control.
190 Now click on the "Volume control" to load the channel mixer dialog. Unmute
191 the "Master" and "PCM" channels and raise the volume as desired. You should
192 now be able to hear sounds played within the virtual machines through your
193 host computer's speakers.