shenylsherry / nilearn-tutorial-brainhack-2016-vienna

Nilearn tutorial for brainhack 2016 at Vienna

Nilearn tutorial for brainhack 2016 at Vienna

When?

The tutorial will take place on Monday, 19th at 11 in Jugendstilhörsaal.

Preparing your computer for the tutorials

No action is required during the tutorial: We will explain the code and present the results. There will be an online version that you can easily follow. However, we strongly encourage you to run the example on your computer, just as we speak.

Installing nilearn

Follow the instructions on the nilearn website. Note that you have to install the latest version of nilearn (2.6) for the tutorial to work. We will provide assistance before the tutorial.

http://nilearn.github.io/introduction.html#installing-nilearn

You will also need the Jupyter notebook. You can install it by running:

pip install jupyter --user

Downloading the data for the tutorial

First, you need to start ipython. Just type ipython in your terminal. Then, copy paste the following lines:

from nilearn.datasets import fetch_abide_pcp

fetch_abide_pcp(derivatives='func_preproc', n_subjects=3, SITE_ID=['NYU'],
                pipeline='cpac')
fetch_abide_pcp(derivatives=['rois_cc200'], SITE_ID=['NYU'], pipeline='cpac')

Downloading extra data

We will show the result of a full analysis on ABIDE. You do not have to run it yourself but, if you want to do it, you will need the timeseries of all ABIDE subjects. Run the command below (after the others) to download them.

fetch_abide_pcp(derivatives=['rois_cc200'], pipeline='cpac')