NIH Blueprint: The Human Connectome Project

How to Access HCP Data

IMPORTANT: Before you begin to use HCP Data, please review the set of available HCP Data Use Terms, and follow the steps to accept the terms that apply to your research.

To access HCP Data, start by navigating to the HCP data home page at www.humanconnectome.org/data. Just below the top panel, you can decide if you would like to:

  • Explore and/or download data in our database platform, ConnectomeDB

or

Clicking on either option takes you to a dialog to register for a ConnectomeDB account.

After you have created an account and are logged in, you must agree to the HCP Open Access Data Use Terms (required for access).

Once these steps are complete, you will launch the HCP Open Access Data Releases page where you can begin to explore and download HCP data by selecting options for groups of subjects from the Q1 release (see "How to download HCP data" below).
Previously released HCP data is also available in the ‘More Datasets’ section.   

Note: Your login to ConnectomeDB times out every 15 minutes. Click the “renew” link to reset the time. (Auto-logout resets ConnectomeDB to the HCP Open Access Data Release page).

How to download HCP data

In order to facilitate access to the very large data files generated on every subject (see HCP Data Sizes), we have prepackaged data into convenient group data packages. Datasets can be downloaded from ConnectomeDB in set packages or users may order all the Q1 data to be sent to them on a hard drive (Connectome in a Box, see below). 

Due to the large file sizes of the data, the HCP uses an Aspera server to dramatically boost data transfer speeds. Therefore, downloading data from the HCP requires you to have the Aspera plugin installed on your browser.

If you have not installed the plugin yet, a warning message will appear at the top of the browser window reminding you that you must Install the Aspera plugin before using any of ConnectomeDB's services, including downloading. An Aspera install help guide is available on the HCP website.

Note: Installing the Aspera plugin to your browser requires you to restart your browser, therefore, we recommend installing the plugin before you explore HCP data in ConnectomeDB.

Upon login to ConnectomeDB, you are brought to the HCP Open Access Data Releases landing page, where you can:

  • Download image data for groups of 1, 5, or 20 unrelated subjects
    • Hover over the illustrations of the subjects to get a short description to help you decide which group is best for your purposes
  • Explore the data for these groups in the ConnectomeDB user interface (currently in Beta testing, not all planned functionality is yet implemented)
  • Download additionally processed group-average data for the group of 20 unrelated subjects
  • Download behavioral data on all subjects
  • Order all Q1 image data via Connectome in a Box
  • Load a custom group of subjects that you created in a previous ConnectomeDB session
  • Browse and download other HCP data that has been released previously

If you choose one of the “Download Now” options for 1, 5, or 20 subjects, you will launch the Download Packages page.

First time Aspera Download Setup

Download Aspera
Download Aspera Connect 3.1

If this is your first time downloading data from ConnectomeDB, before you start selecting packages to download, we highly recommend setting up the preferences in your Aspera Connect plugin to download to the appropriate place on your local or network hard drive.

Note: the default Aspera Connect download location is your Desktop, which is likely not where you want your HCP data to go!

Please refer to the Aspera installation guide for further help.

Downloading HCP data packages

Now that you have Aspera setup to download to the correct location, go back to the “Downloading Packages” page in your browser.

Here, you can filter the image data available for download by format and modality by clicking the “Select Format” and “Filter by modality” buttons. To make selections for download, click the “add to queue” icons to the left of each dataset.

The total size of the data you have queued for download is at the upper and bottom right. Use this calculation to check against your available hard drive space to be sure you have enough space available for the files you intend to download.

When you are done making your selections, click the Download Packages button at the upper right. A popup will remind you again what packages you selected and the total size of the files. Clicking “Download Now” will automatically open Aspera Connect and launch the download.

Note: If you have not setup Aspera Connect, as described above, by default the data will start downloading to your Desktop. If this not where you want the data to go, we recommend stopping the download by clicking the “X” button to the right of the download progress bar. Click the gear icon at the bottom left of the Aspera Connect: Transfers window to launch the Aspera preferences window (see above).  Once you set the preferred download location, you will need to relaunch your download in ConnectomeDB, using your browser’s back button to return to the “Downloading Packages” page.

If the download does not start automatically, use the link on the Download Package Launcher page in your browser to restart.

Once downloading has started, the blue bar in the Aspera Connect: Transfers window will show your progress (per subject file, not your overall progress).

Obviously, the more subjects and packages you selected for download, the longer your download will take (remember, this is big data!). 

This is why we are offering the “Connectome in a Box” option for those who want data on many subjects.

Handling downloaded HCP data

Now that you have downloaded the data you want, here’s some tips for handling the data:

  • Each download package consists of a .zip archive, and an md5 checksum. After you download the data you want, you can use the md5 file to verify the integrity of your downloaded file.
  • To unzip the downloaded .zip archives, for Windows users we recommend using a utility such as 7-zip (available free) so that the directory structure of the unzipped files remains intact. The built-in unzip capabilities of Linux and MacOSX can be used as they do not affect the directory structure of the unzipped files.
  • Once the archives are downloaded and unzipped, many of the component files are gzipped (.gz files). You will need to unzip all.gz files in order to use them. For this, you need an application that is compatible with gzip. For Windows users, we again recommend 7-zip. Linux has support for gzip built in, and Mac users can use the Mac Gzip utility.
  • Downloaded HCP data unzips to a set directory structure that is detailed in Appendix 3: File Names and Directory Structure for Unprocessed and Preprocessed HCP Q1 Data. The directory structure for downloaded HCP data is identical to what is provided in HCP_Q1 Connectome in a Box.
  • If you have downloaded a large amount of HCP data, we recommend sharing the data locally at your research institution. This will save download and organization time for your colleagues and relieve some of the burden on the ConnectomeDB download bandwidth available to other HCP users.

We are compiling a set of best practices for long-term data storage, which can be seen in our online documentation.

How to order the Q1 dataset as a "Connectome in a Box"

An attractive option for getting Q1 HCP data is “Connectome in a Box”. This option allows users to order a hard drive containing the complete Q1 imaging data from the HCP (HCP_Q1 data) “at cost” (approximately $150/Quarter of data + shipping costs) and have it shipped to their address. 

HCP_Q1 Connectome in a Box can be securely ordered from the HCP website.
Connectome in a Box contains both unprocessed and preprocessed NIFTI image data formats.  The data is loaded on a SATA hard drive formatted to your choice of operating system (MacOSX, Linux, or Windows).

Once the user (or group of users) receive the drive, it can be added into a network storage unit and made available to all on the user’s local network. Alternatively, the drive can be simply plugged right into a computer and used as you would an external hard drive. For this option, we recommend purchasing a hard drive enclosure. We have an enclosure available (at cost) that you can purchase when you order Connectome in a Box, although you may wish to buy your own elsewhere.

Each time a new dataset is released, users may wish to order another drive with that quarter’s HCP data loaded onto it. We are currently exploring the option to recycle previous Connectome in a Box drives for subsequent releases (more on that when Q2 is released).

As HCP data is updated, depending on the amount of data and related logistics, we may recommend updating the HCP_Q1 Connectome in a Box via download from ConnectomeDB.