Lin4Neuro

Download

• Username is “brain” and Password is “lin4neuro” for each VM.
• file is provided via Google drive

Version	Type	File	size	md5
L4N 22.04	Standard	l4n-22.04.2-standard-en_20230702.ova	12.7GB	e8abd5d25690feb730a6c065910c175e
L4N 22.04	Compact	l4n-22.04.2-compact-en_20230702.ova	3.8GB	6db8c05d4413fb12b695355437394a25
L4N 20.04	Standard	l4n-20.04.6-standard-en_20230702.ova	12.3GB	2e10879cff807f92d1ec2c3351e91ec5
L4N 20.04	Compact	l4n-20.04.6-compact-en_20230702.ova	3.7GB	dcfdb6ea63d2cd993dedfe7d94466d37

• Lin4Neuro based on Ubuntu 16.04/18.04/20.04/22.04



• Lin4Neuro based on Xubuntu 14.04



• Lin4Neuro based on Xubuntu 12.04

ChangeLog

• 24 Sep 2022: l4n-22.04.1-amd64-20220924 was released. This version is based on Ubuntu 22.04.1 LTS
• 10 Aug 2021: l4n-20.04.2-amd64-20210810 was released. This version is based on Ubuntu 20.04 LTS mini.iso.
• 16 May 2020: l4n-18.04.4-amd64-20200516 was released. This version is based on Ubuntu 18.04 LTS desktop.
• 31 Jan 2017: l4n-16.04-x64-en-20170329 was released. This version is based on Ubuntu 16.04 LTS mini.iso.
• 18 Jan 2016: l4n-14.04-x64-en-20160118 was released. Now Lin4Neuro is based on Ubuntu 14.04 LTS mini.iso.
• 15 Dec 2014: Lin4Neuro based on Xubuntu 14.04 was released. I will keep maintaining Lin4Neuro based on Xubuntu 12.04, too.
• 12 Dec 2014: l4n-12.04-x64-en-20141212 (64bit) was released.
• 13 Jun 2014: l4n-12.04-x64-en-20140612 (64bit) was released.
• 13 Mar 2014: l4n-12.04-x64-en-20140313 (64bit) was released.
• 31 Aug 2013: l4n-12.04-x64-en-20130829 (64bit) and l4n-12.04-x86-en-20130829 (32bit) were released.
• 17 Jan 2013: l4n-12.04-x64-en-20130117 (64bit) and l4n-12.04-x86-en-20130117 (32bit) were released.
• 01 Dec 2012: Lin4Neuro based on Xubuntu 12.04 was released. Now you can get Lin4Neuro based on both Ubuntu 10.04 and Xubuntu 12.04.
• 18 Sep 2012: lin4neuro-lucid-amd64-20120918 and lin4neuro-lucid-i386-20120918 were released.
• 07 May 2012: lin4neuro-amd64-20120507 and lin4neuro-i386-20120507 were released.

What is Lin4Neuro for?

Lin4Neuro is just for you, if you…

• found a nice neuroimaging analysis software package, but gave up just because it runs under Linux.
• have been interested in using Linux, but doesn’t know what to do first.
• installed Linux by yourself, only to find it difficult to configure the software packages you want to use for your circumstances.

With the help from my colleagues and friends, I made a customized Linux which is optimized for neuroimaging analysis.

Lin4Neuro (L4N) is based on Ubuntu with XFCE desktop environment. Lin4Neuro includes many useful neuroimaging software packages. The list of packages can be found here.

These software packages are well known and widely used for neuroimaging analysis. They are also distributed under the GNU GPL (General Public License), BSD (Berkeley Software Distribution) license, or any license which states that the packaged software can be redistributed for research purposes provided there is no financial return.

With Lin4Neuro in one’s hand, one can access neuroimaging software packages easily, and immediately focus on analyzing data. Lin4Neuro can be a good primer for beginners of neuroimaging analysis or students who are interested in neuroimaging analysis. It also provides a practical means of sharing analysis environments across sites.

Hardware requirement

Lin4Neuro is based on Ubuntu, so the system requirement is the same as Ubuntu. However, you need much more powerful CPU and memory to run neuroimaging software packages included in Lin4Neuro. System requirements for Freesurfer might be useful: (Note: If you plan to use virtual machine, memory should be larger than 8GB)

• A 2GHz or faster processor
• At least 8GB of RAM
• 3D graphics card (with a GPU and its own graphics memory) with accelerated OpenGL drivers
• Screen resolution: Full HD (1920×1080) or bigger

Getting Lin4Neuro

1. Download

   You can get the Lin4Neuro from the top of this page.
   
   Lin4Neuro is 64bit OS, so you need hardware compatible with 64bit OS (You won’t have problems with recent hardware). The size is quite huge (~16-18GB), so downloading may take some time. Please be patient.

2. Setting up Lin4Neuro
   • Use VirtualBox

   Lin4Neuro virtual machine is configured to run instantly on VirtualBox 6.1. After downloading l4n-*.ova, From VirtualBox menu, select file -> import applicances… and select the downloaded ova.

   • Booting Lin4Neuro
     • From VirtualBox

       It is simple to boot from virtualization software. Just turn on your VirtualBox and you will see the Lin4Neuro booting in a minute. Username is “brain” and password is “lin4neuro”.

Using Lin4Neuro

1. GUI (Graphical User Interface) Menu
   All of the GUI software can be reached from the menu. I customized the menu so that Windows users can easily access the software packages. The “Start” button is on the bottom-left. By clicking the button, the customized menu pops up. On the top of the menu, you see “Neuroimaging”, under which several neuroimaging software packages are listed.

   

2. CUI (Commandline User Interface)
   The icon next to the start button is the shortcut to the “terminal.” Sometimes (actually often), you need to run various programs from terminal.

   For example, if you want to run MRIcroGL from the terminal, type the following in the terminal window. (You don’t have to type “$”)

   $ MRIcroGL
   

   That brings up the MRIcroGL window.

3. Use installer to several neuroimaging software packages

When the first version of Lin4Neuro was developed, it included all of the neuroimaging software packages. Nowadays it is not possible to include all of them because packages are getting bigger and bigger. Then, I changed the strategy to provide installers for large packages such as 3D Slicer, ANTs, AFNI, FreeSurfer, MRtrix3, or FSL. I also provide standalone version of CONN and SPM.

You see the shortcut “installer” on Desktop. In that directory, installers are provided.



4. Tutorials
   Professor Chris Rorden kindly provided excellent MRI analysis tutorials. It can be accessed from Neuroimaging menu, and tutorial data itself is stored under home/tutorials.

License and Citation

Lin4Neuro itself is distributed under GPL. However, you need to agree the licenses of each software packages to use them.
As of sample dataset by Chris Rorden, I got permission from Chris to distribute the dataset.

If you find Lin4Neuro useful and use for your data analysis, please cite the following article in your paper.

Nemoto K, Dan I, Rorden C, Ohnishi T, Tsuzuki D, Okamoto M, Yamashita F, and Asada T. Lin4Neuro: a customized Linux distribution ready for neuroimaging analysis. BMC Medical Imaging 2011, 11:3

Acknowledgment

• Lin4Neuro employs NeuroDebian
  Lin4Neuro employs NeuroDebian repository. Among the software packages in Lin4Neuro, I setup and configured MRIConvert through NeuroDebian. I appreciate much for their great contribution to this field.
  
  

• Grant
  This work was supported in part by Health and Labor Sciences Research Grants, Research on Psychiatric and Neurological Diseases and Mental Health.
  I am grateful to Dr. Masato Fukuda and Dr. Ippeita Dan for their understandings and encouragement for this project.

• Professor Chris Rorden kindly provided sample dataset and excellent tutorials. He also gave me many useful suggestions. I am so grateful for his help.
• I also would like to express my gratitude to Mr. Daisuke Tsuzuki and Mr. Masato Kobayashi for their help.

Feedback

I would like to hear your opinion or requests about Lin4Neuro. You can reach me at kiyotaka_at_nemotos.net

© 2010-2022 by Kiyotaka NEMOTO