Chapter #2: Downloading the Data
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
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')
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.
Click here for a video demonstration of how to download the data.