Database Access

COINS

The ABIDE dataset is the first dataset to be shared publicly through the COINS Data Exchange application. The Data Exchange is a web-based data sharing environment where researchers can browse the extensive COINS database for data related to their research. Requests to share data can then be made to the data's owner. The Data Exchange offers a messaging and approval system to facilitate communication between researchers. Once a request is approved by the data-owner, that data can be downloaded through the Data Exchange download center.

Since the ABIDE dataset is public, it is pre-approved for sharing in the Data Exchange. This means that the ABIDE data will be made instantly available for download upon requesting it. To request ABIDE data through the COINS Data Exchange, follow these simple steps:

  1. In Firefox or Chrome, click here to load the COINS site.
  2. Create a user account if you do not already have one.
  3. Log in.
  4. Accept the usage agreement.
  5. Click 'Browse Available Data'.
  6. Select the data that you want and add it to your cart.
  7. Click 'Send Request' once you have selected all the data that you want.
  8. That's it. Download links will now appear next to each dataset that you requested.
  9. To come back to download later, simply go to coins.mrn.org/dataXchange again and click on 'Download Shared Data'.

LORIS

LORIS offers the ability for researchers to view and download the ABIDE dataset in part or in whole through its Data Querying tool. Both behavioural and imaging metadata can be queried and output as spreadsheets in various formats. The raw imaging files can also be packaged as compressed data files available for download through a variety of web browsers (Firefox, Chrome, Safari). Queries can be performed for predefined populations, producing manageable subsets of data.

To request ABIDE data via LORIS:

  1. Click here to load the LORIS site.
  2. Log in with username abide and password abide_2012
  3. In the Querying tool, choose the variable that you wish to download from the pulldown, and click on the download tab. Follow the instructions in the browser for more details on restricting populations.
  4. Feel free to make use of the Imaging Browser to view images via the web.

LONI IDA

The LONI IDA, which houses imaging and clinical data for dozens of single and multi-site studies, has added the ABIDE dataset as a publicly shared study. The IDA is a web-based data archive environment where researchers can store, search and share neuroimaging and clinical data. Subject attributes, such as age, gender and diagnostic group along with image-related attributes can be used in searching for data of interest and once data are selected images may be downloaded. Collections of data stored in the IDA can also be ported into the LONI Pipeline workflow environment where a wide variety ofsoftware and tools are available for image processing and analysis.

Because the ABIDE dataset is anonymized, a separate ABIDE Data Sharing Agreement is not required for obtaining ABIDE data. However access to the IDA does require an active user account. To access ABIDE data through the IDA, follow these simple steps:

  1. Click here to load the LONI IDA site.
  2. Register for a user account if you do not already have one. 
  3. Log in.
  4. Use one of the Search options to select imaging data OR navigate to the Download section to download phenotypic data or study-related documents.

NITRC-IR

The ABIDE dataset joins a number of publicly accessible datasets available in the NITRC IR (including the 1000 Functional Connectomes 'Classic' release, ADHD-200, CANDIShare). The NITRC-IR provides a XNAT database version of select datasets previously available on NITRC.org as bundled 'tar' files in the 1000 Functional Connectomes resource.

The ABIDE dataset is publicly available, but requires users to register with the 1000 Functional Connectomes project at NITRC.org. To access ABIDE data through the NITRC-IR, follow these simple steps:

  1. Click here to load the NITRC-IR site. Note that this can also be reached from the "ABIDE Downloads" link on the on the left-side tabs of the 1000 Functional Connectomes Project page . Make sure to be logged in as a registered user of NITRC.org and a member of the 1000 Functional Connectomes resource; or the NITRC-IR will redirect you to the appropriate registration pages.
  2.  From the NITRC-IR ABIDE page, you have access to all 1,112 individual subjects. Click on a subject (i.e. Caltech_51456) and you will see a subject summary and a link to the 'MR Session'; accessing the MR Session will provide a summary of the session and show some details of the data available for that subject. From here, you can download the individual datasets from the 'Download' Action on the right of the page.
  3. More importantly, instead of downloading many tar files (or individual subjects), the NITRC-IR provides the ability to search for groups of subjects that meet specific criteria, and then download of that specific group of subjects. NITRC-IR supports a number of ways to search, for more details, click on NITRC.org Help.

NIDB

Neuroinformatics Database is a modular, scalable, and easy to use database that installs in less than 1 hour. It includes data request, MRI QA, dicom receiver modules and can also store and query any modality of imaging data, including full assessments and phenotypic data. Automatic pipeline processing is also available as a module.

ABIDE data is not available for download from the NIDB website, but data can be imported into an NIDB installation once data has been downloaded from other sites. To use NIDB to sort and serve ABIDE data, follow these steps:

  1. Download the NIDB virtual machine, or download and install the tarball. (http://nidb.sourceforge.net)
  2. Download the ABIDE tarballs, and unzip.
  3. Run the import scripts for imaging and phenotype data.
  4. Complete import instructions are available at http://nidb.sourceforge.net/?page_id=133