Lin4Neuro

10 Aug 2021: Lin4Neuro based on Ubuntu 20.04 is released (for Virtual machine images only).

  • Lin4Neuro based on Ubuntu 16.04/18.04/20.04
  • L4N-xenial-screenshot

  • Lin4Neuro based on Xubuntu 14.04
  • L4N-trusty-screenshot

  • Lin4Neuro based on Xubuntu 12.04
  • l4nscreenshot

You can download the latest version of Lin4Neuro from here.

What’s New

  • 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 18.04LTS with XFCE desktop environment (L4N based on Ubuntu 14.04/16.04 is available, but development is stopped). 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 18.04LTS, 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 4GB of RAM
  • 3D graphics card (with a GPU and its own graphics memory) with accelerated OpenGL drivers
  • 17″ or bigger monitor

Getting Lin4Neuro

  1. Download

    You can get the iso image / virtual machine of Lin4Neuro from here.

    Lin4Neuro is 64bit OS, so you need hardware compatible with 64bit OS (You won’t have problems with recent hardware). The size of the iso file is around 3.0GB, so downloading may take some time. Please be patient.

  2. Setting up Lin4Neuro

    After downloading the files, you have some options to setup 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.

    • Make a live USB drive
    • You can make a live USB drive using Rufus, Universal USB installer, or others. Please prepare an USB flash drive with more than 4GB.

  3. 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”.

    • From USB flash drive

      It depends on the PC you use, but try to push “F12” or “F11” right after turning on your PC. This prompts the screen in which you can select to boot from USB. If not, you may need to get in th BIOS set up. Please read the instruction of your PC.

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
  4. 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.

  5. 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.

  • 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.

Some comments from Michael Hanke

I got several comments from one of the NeuroDebian developers, Michael Hanke. I appreciate his comments and think it is useful to share his comments with everyone.

  • It should be noted that unlike all the properly integrated parts of the system (from Debian, Ubuntu or NeuroDebian) any custom software installation will not be updated by the system’s package manager.
  • The NeuroDebian projects offers virtual machine images where users can easily install Matlab in a matter of minutes, and it also offers a packaged version of SPM that can be updated with built-in system tools.

Feedback

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

© 2010-2021 by Kiyotaka NEMOTO

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14 thoughts on “Lin4Neuro

  1. ピングバック: Analice la neuroimagen con Linux. Una distribución específica. - Sistemaoperativo.top

  2. ピングバック: Analyse de la neuroimagerie avec LInux. Une distribution spécifique.

  3. Thank you for your great work.
    I have downloaded l4n-12.04-x64-en-20140612.iso twice because the md5 checksum was not matched, which made the installation failed.
    I am trying to use the Connectome Mapper.
    How can I get the correct iso file? Could you provide anothor link or links to previous version such as 20140313?
    Thanks a lot

    • Thank you for your comment.
      I checked the md5 of the l4n-12.04-x64-en-20140612.iso on the server and it was matched.
      Since the file size of the iso image is big, sometimes downloading fails.
      Could you try downloader like Down’em All or other?

      If it doesn’t work, please let me know and I’ll look for another way to deliver the iso.

  4. Great work!! It’s the end of distro-hopping at work! I’ve been following your distributions since the version based on ubuntu 10.04 LTS. I think this last version 20140313 (based on xubuntu 12.04.4 LTS) is the best.
    Best,
    FV

    • Dear Fernando,

      Thank you very much for your compliment. Positive feedback is the motive of keep developing Lin4Neuro.
      If you have any requests, please let me know.

      Kiyotaka

  5. Hi,
    thank you for this great work!
    Is it possible to integrate Freesurfer by using the Remastersys Program?

    Best wishes!

    • Hi,

      Thank you for your comment.
      Yes, it is possible to integrate Freesurfer using Remastersys.
      You may need to remove some unnecessary applications so that the file size of iso is less than 4GB.

      I don’t include Freesurfer into Lin4Neuro just because it requires registration.
      However, I get several requests from many, so I will check the license and consider including Freesurfer.
      (Of course every user needs to register in the Freeesurfer website.)

    • Hi,

      Thank you for the request.
      I will look at the tool and try to integrate it into Lin4Neuro.
      Please wait for a while and I will let you know when it becomes available.

  6. Hi. What is the username / password to login to lin4neuro? Booting works fine but is useless without a login…

    • Could you tell me which version of Lin4Neuro did you download?

      Sometimes remastering doesn’t work well and it requires username though it shouldn’t be…

      Just in case, login should be “custom” and password should not be required…

      I will check all of the version, but if you let me know, that’s helpful.

      Best regards,

      Kiyotaka

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