Child pages
  • OASIS on XNAT Central

Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

To access datasets from any of the three OASIS projects, you must first sign the data use agreement located at oasis-brains.org. Within one week of completing this form, you will be sent an invite to XNAT Central at the email address you provided. You can then follow the XNAT Central sign-up process and view the data. If you already have an XNAT Central account at your provided email address, you will be granted access to the OASIS-1, 2, or 3 projects on Central, depending on what you selected in the data use agreement form.

For more information on registering an XNAT account, see User Registration and Accounts in XNAT.

Note: Requesting OASIS project access directly from XNAT Central will not enable you to access the data immediately. You must fill out the data use agreement first to receive project access.

...

If you click on the "Options" button (outlined in red below) you will see a list of options for the data listing. 

Image Modified

Options → Spreadsheet will enable you to download the current table in a .csv (comma-separated) spreadsheet format.

Options → Edit Columns will display a column editor window that enables you to select which columns to display in the table. 

Image Modified

The list on the left contains the currently visible columns. The list on the right contains the fields available to be added to the current list. Use the left and right arrows in the center to move fields between the lists, and use the up and down arrows on the left side to rearrange fields in the Current Fields listing. Press Submit to display the results. 

Note: Not all fields listed under Available Fields will have data to display. For example, OASIS data does not contain tumor information, so the field "Custom Field:tumorlocation" will always be blank.

Filtering OASIS Data Using Searches

In addition to viewing the full list of subjects from the project page, you can view a subset of subjects based on a search result. A standard search can be useful if you're looking for a single subject, session, Freesurfer result or PUP result based on an ID or name that you have. For details, see Using the Standard Search.

If you want to filter a subjects, sessions, Freesurfers or PUPs based on criteria that you choose, use an Advanced Search. For details, see Using the Advanced Search.

Downloading Data from XNAT Central

Using the

...

Web User Interface

Note: We have been experiencing intermittent issues with this download method. If you experience problems with this method, please see Downloading Data Using the Command Line.

OASIS data can be downloaded directly from the XNAT Central website using your web browser. For more information, see How To Download Image Data From XNAT Projects.

...

Using the Command Line

OASIS data can be downloaded using scripts called from a Windows, Mac, or Linux command line. This can be useful if you'd like to automate downloading or organize files.

For example scripts and instructions on how to use them, visit the oasis-scripts repository on Github.

Creating Usable Spreadsheets for Downloading Data

The example OASIS download scripts on the Github page require a list of OASIS subjects experiment_ids as an input. This can be created by including the "SubjectMR ID" column in your column view, and downloading the result via the Options → Spreadsheet option described above. Once you download a spreadsheet, remove all columns from it except for the "SubjectMR ID" column and save it as a .csv file. This can be done In Microsoft Excel by selecting Save As and choosing "CSV (Comma delimited) *.csv" as the file type. 

If you save a file using Microsoft Excel, you must convert it to Unix format before using it as input to a script. If the file is incorrectly formatted, you will receive "Illegal character" errors when you run the script. Instructions for doing this conversion can be found in the "Note on Unix file formatting" section of the oasis-scripts README.

Writing Custom Scripts Using the REST API

More advanced users can write their own scripts to download data from XNAT Central via the REST API. For more details on using the XNAT REST API to download scan data and processed image data, see How To Download Files via the XNAT REST API.

...