Chapter #2: Downloading the Data

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Overview

The data we will use for this tutorial comes from the open-access repository Openneuro.org. From the Openneuro homepage, click on Dashboard, which will load all of the available datasets. Select the dataset “fMRI: resting state and arithmetic task”, which should be listed in the first page that comes up. If you are unable to find it, use the search bar to look for the string “arithmetic”; it should be the first result that is returned.

Click on the sub-01 folder, and then click on anat. Click the Download button next to the file “sub-01_T1w.nii”, which will begin downloading the file. Next, click on the func folder to look at its contents, and download the file “sub-01_task-rest_bold.nii.gz”.

If these files have been downloaded to your Downloads folder, open a Matlab terminal and type the following:

cd ~/Desktop
mkdir CONN_Demo

This navigates to your Desktop and creates a new folder called CONN_Demo. This is where we will store our data and do our analyses. To organize the data into two folders within the CONN_Demo directory, type the following from your Matlab terminal:

cd CONN_Demo
mkdir sub-01/func
mkdir sub-01/anat

Which will create the folders func and anat within a folder called sub-01. To move your downloaded files into their corresponding directories, type the following:

movefile('~/Downloads/sub-01_func_sub-01_task-rest_bold.nii.gz', 'sub-01/func')
movefile('~/Downloads/sub-01_anat_sub-01_T1w.nii', 'sub-01/anat')

Type ls sub-01/anat and ls sub-01/func to make sure that the functional data is now located in the func directory, and that the anatomical data is located in the anat directory. If so, you are now ready to begin using the CONN toolbox, which we now turn to.

Video

Click here for a video demonstration of how to download the data.