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neured edited this page Jan 5, 2019 · 55 revisions

How to Process MRI Images:

  1. Beginner's Guide to Command Line Interface
  2. More about the Command Line Interface
  3. NITRC, a source for neuroimaging software and data.
  4. Before you begin
    • Computer setup and Applications
  5. Preprocessing and processing images
  6. Hippocampus Segmentation

Before You Begin

Generally neuroimaging computing is done on Linux or macOS. You may need to be logged in as root to install many of these programs, depending on the permissions of the directory on which you are installing. The following are specifics about operating systems I currently use to run neuroimaging analyses:

macOS (10.12+)

You should install XCode first before beginning any of these other tasks. The version of XCode will vary, depending on your OS version XCode

In order to have access to root user you have to directly enable the option, for instructions refer to this page here. If you are on a university or company managed computer, it's a good idea to talk with your IT administrator before installing any software (if you have administrator access).

Ubuntu 18.04.1 (Bionic Beaver)

Windows 10

With the Windows Subsystem for Linux activated and Ubuntu installed you can use many common MRI applications. If you are using Windows it may be easier to log in as the Administrator for all of these downloads. If you are using a managed computer, you will likely need your IT administrator to install any software.

Notes Regarding Windows

Some imaging programs (MANGO, dcm2nii, mricron, and some functions of ANTs) can be installed onto Windows easily but you will quickly find barriers between programs. The neuroimaging community likes to run things on Linux or macOS (although SPM runs well on Windows so many people who do only fMRI research use Windows). If you are interested in having these programs on your own computer I suggest a free installation of Linux. Ubuntu, Mint, Debian, CentOS, and others work well. Ubuntu is quite easy to use and learn. If you aren't fully committed to using just Linux you can run it in a Virtual Machine or partition your drive to dual boot, which allows you to run Linux or Windows upon restarting your computer each time. NeuroDebian is a VM that can be installed and run without too much difficulty. I won't reproduce the installation instructions here.

Another option mentioned previously is with Windows 10 and the Windows Subsystem for Linux. Follow those instructions to get this useful tool installed. Once you enable the WSL, you can easily install your Linux distribution of choice. There are some limitations to the WSL relative to a "pure" installation of Linux but it gives access to a number of the tools previously unusable in Windows. Windows Subsystem for Linux Documentation

Recommended MRI and Useful Software

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