Tutorial 2: Neuroimaging software installation


At a great number of research facilities powerful cluster computers are used for analyzing neuroimaging datasets, yet if the silicon industry keeps its promise the next decade of computing will bring cluster power to the office environment. Already it is possible to house a powerful 4/8/12/16 core computer under your desk (even without having to listen to the permanent roar that is equivalent to a 2100 Watts vacuum cleaner). In 2011 this can be scaled further up to 20 cores in a single workstation. In addition, graphics cards are more and more becoming general purpose processors that are suitable for massive parallel computations. This could speed up our work significantly, e.g. with image registration and ultimately with the entire analysis pipeline.

Most researchers want a personal workstation with which data van be analyzed and visualized. Setting up a neuroimaging workstation offers a challenge for those who are less technically inclined and the job is often handed over to the tech-support of an institution. However, it may be quite challenging to explain what features you like to have installed on your workstation.

In this tutorial some suggestions and solutions are provided for setting up a neuroimaging workstation. If you will not set up software yourself, you may refer this tutorial to your IT department. Please note that there is a separate tutorial on hardware recommendations.

I Windows, Mac or Linux?

Which operating system is best suitable for a neuroimaging workstation? Although this question may spark strong emotions in some people and answers often resemble a personal religion, here an attempt is made to provide an answer.

II Red Hat, Fedora, CentOS

If you are not choosing MacOSX, Linux is recommended as the primary analysis platform, but which distribution should one choose? The decisive factor for choosing a distribution is if the neuroimaging software of your choice will run on it.

VII Free Scripts

Some useful scripts that I created or adapted. Feel free to (re)use these scripts for any non-commercial application.

III Dual booting

Do you want to run more than one OS? That can of course be done? But there are several ways of doing this. This section explains the options and pro's and cons for a dual/multi boot environment.

IV Virtualization

Virtualization is a new technique that allows you to run multiple operating systems at the same time. When should you use dual booting and when is it better to run a virtual machine?

V Software Installation

Once you have set up your operating system, you will have to start installing the applications of your choice. This section provides some recommendations.

VI Neuroimaging software list

There is a long list of neuroimaging software packages available. This section will list the most common packages for functional MRI analysis and provides a link to a searchable database that includes all neuroimaging software.