NeuroDebian

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I recently came across a great resource for people involved in neuroscience research. It’s called NeuroDebian; it’s a Debian neuroscience repository. Debian is a popular Linux distro; what is likely the most popular consumer Linux distro – Ubuntu – is an offshoot of Debian. Those comfortable with one likely will be comfortable with the other. I know that this does not directly apply to the Mac but you will deal with Linux at some point if you do enough neuroimaging (although most of the software are available as Mac native packages) so it’s worth becoming familiar with it. If you are comfortable with the command line in OS X, you will be comfortable in Linux.

The repository includes a number of neuroscience packages (programs) for easy installation and update (e.g., FSL, MRIcron, AFNI, 3d Slicer, ITK-SNAP). You can add the repositories to your existing Linux installation (Debian or Ubuntu) or you can download a Debian virtual machine, which allows you to try out Debian and the repository without altering your current system. To use this virtual machine you need to install VirtualBox (a free download for Windows, Linux, Mac, or Solaris). The setup is easy and explained on the neurodebian website.

Here’s what it looks like running on my Mac:

NeuroDebian_6.0.2_64bit2

I haven’t had an opportunity to use it much yet but I wanted to spread the word about this service. I’ll post more about it once I have an opportunity to use it more. It makes the installation and management of many popular neuroscience programs easy (for example, it can be as easy as: sudo apt-get install ants). Unless you are doing very graphics heavy 3D imaging work, virtualizing neurodebian will have sufficient performance on modern computers.

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About Jared Tanner

I have a PhD in Clinical and Health Psychology with an emphasis in neuropsychology at the University of Florida. I previously studied at Brigham Young University. I am currently a Research Assistant Professor at the University of Florida. I spend the bulk of my research time dealing with structural magnetic resonance images of the brain. My specialty is with traditional structural MR images, such as T1-weighted and T2-weighted images, as well as diffusion weighted images. I also look at the cognitive and behavioral functioning of individuals with PD and older adults undergoing orthopedic surgery. Funding for the images came from NINDS K23NS060660 (awarded to Catherine Price, University of Florida). Brain images may not be used without my written permission (grant and software requirements).