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Installation on Windows

Git version control

Go to http://git-scm.com/

Click on the Downloads for Windows link at the bottom right.

Download the file they propose, with a filename something like Git-2.9.3.2-32-bit.exe.

Run the file to start the installation.

We suggest you accept the defaults, except the sceen called “Adjusting your PATH environment”, where we suggest you choose the option “Use git from the Windows Command Prompt”.

The Atom text editor

Go to https://atom.io/

Download the Windows installer, run.

The Hydrogen plugin for Atom

Installing this plugin is complicated, because you will need:

  • Atom to be running with Python version 2 as the default Python version. That is inconvenient, because later on we’ll need Python 3 for the class;
  • an installation of a particular Microsoft Windows compiler program. A compiler is software that takes programs written in human-readable format and “compiles” them into instructions for the computer cental processing unit (CPU).

See https://atom.io/packages/hydrogen for more information. What follows is a recipe:

  1. Python 2.7: go to: https://www.continuum.io/downloads. Click on the Windows symbol for Windows downloads. Select the 64-bit installer for Python 2.7, download, and install. Choose to install for “Just me”, and leave the defaults as they are for the rest of the installation dialog boxes. Now you have a version of Python 2.7;
  2. You are going to install Microsoft Visual Studio 2013 Express. This is a free compiler from Microsoft. You need the 2013 version, so be careful not to install a later version, such as the 2015 edition. Go to: https://www.microsoft.com/en-US/download/details.aspx?id=44914. Choose wdexpress.exe to download. Run this installer. Accept all the defaults. Reboot when the Visual Studio 2013 install has finished. You now have the compiler you need;
  3. You can now install the Hydrogen plugin. Start the Atom editor. Go to the File menu, Settings, select +Install, type “hydrogen” in the search box, and click the Packages button to search. When hydrogen comes up, click the Install button. Wait a few minutes. If there is an error, please come and find us for help. Close Atom.
  4. Now install Python 3. Go back to: https://www.continuum.io/downloads. Click on the Windows symbol for Windows downloads. Select the 64-bit installer for Python 3.5, download, and install. Choose to install for “Just me”, and leave the defaults as they are for the rest of the installation dialog boxes. Now you have a version of Python 3.5;

Test the Hydrogen plugin by starting Atom as you normally would. Make a new text file and save it somewhere as test.py. Type a = 10 and press Alt-Shift-Enter to run this line in Hydrogen. After a few seconds, you should see that Hydrogen started a new Python 3 kernel, and there will be a tick after the a = 10 line. Or you may have got a small menu asking if you want a Python 2 or a Python 3 menu. If so, all is probably well. Otherwise, come and ask your instructors.

Python and packages

You install Python 3 and many of the packages you need in the last step, when you installed Anaconda3 (the version of Anaconda with Python 3.5).

The last package you need is nibabel.

Open git bash (this should have been installed with git).

Type which python (and return) to see the version of Python that bash is finding. It should be something like /c/Users/your_user/Anaconda3/python (note the Anaconda3).

Now type:

pip install nibabel

Check the installation worked with:

ipython

then, from the IPython In [1] prompt:

import nibabel

That should return without an error. Congratulations, you’re ready for the classes.