Attention

This documentation is under active development, meaning that it can change over time as we refine it. Please email store.star.help@monash.edu if you require assistance, or have suggestions to improve this documentation.

XNAT

Monash-XNAT (xnat.monash.edu) is the Monash University instance of the popular neuroimaging archive system, XNAT (xnat.org). It archives imaging data acquired on Monash’s clinical MR/MR-PET/CT scanners.

This page outlines the data integration between Monash University XNAT and MASSIVE M3.

Create an account at Monash-XNAT

  1. Register for a new account on Monash-XNAT.

  2. You will receive an email to verify your email address.

3. After verifying your email, wait for a Monash-XNAT administrator to enable your account before you can log in. Please email store.star.help@monash.edu if your account is not enabled after the next working day.

Request to create a project at Monash-XNAT

  1. Please fill out the Monash-XNAT Project Request Form:
    • You can access this form if you have Monash affiliation. Please email store.star.help@monash.edu if you don’t have Monash account and would like to request to create a project at Monash-XNAT.

    • This form is designed to collect the information needed for creating a new project on Monash-XNAT. It has multiple sections, including information about the research project, principle investigator, team who will have access to it on XNAT, data sensitivity classification and etc.

    • Note that it is requires to be filled out by a project investigator or project coordinator.

  2. A Monash-XNAT administrator will review it and email you to confirm the project registration.

Mirroring data from Alfred-XNAT to Monash-XNAT

  1. Refer to the low risk guide document to check whether your research fits into a low risk category at Alfred Health. Accordingly, apply for ethics approval following steps provided in the link here

  2. The Alfred Ethics Committee will review your application. They will provide you with the Human Research Ethics Committee (HREC) number if it is approved or contact you for further information.

  3. Assuming the HREC number is assigned to your research at Alfred Hospital, use it to fill in a ‘Radiology Resource’ form. In this form you can specify what types of data you want to transfer from Alfred-XNAT to Monash-XNAT.

  4. The whole process cost will be calculated by the Alfred radiology team for your information.

  5. A project will be created at Alfred-XNAT to include the data required for your research.
    • All data in Alfred-XNAT are anonymised. A hash-key is generated in the anonymisation method that is used as a subject-id. It allows linking of multiple records/scans of the same subject. Below is a sample order of data per subject:
      • ‘SUBJECT HASH KEY ID’
        • scan date X

        • scan date Y

        • scan date Z

Note

If you already have a Monash-XNAT account, skip the next step

  1. Create an account at Monash-XNAT

Note

If you already have a Monash-XNAT project, skip the next step

  1. Request to create a project at Monash-XNAT

  2. Since Alfred-XNAT is within a firewall, the Alfred team has set up Monash VPN for allowing data transfer to Monash-XNAT. Following that, XNAT’s plugin, xsync, can be used by XNAT administrators to transfer data from Alfred-XNAT to Monash-XNAT using project-IDs at each end.

  3. Please contact Robin Lee at Ro.Lee@alfred.org.au for any enquiries related to processes at Alfred Hospital’s end.

Pulling Data from Monash-XNAT to MASSIVE M3

The steps to download data from Monash-XNAT to MASSIVE M3 are:

Note

If you already have an M3 account, skip the next step

  1. Create an account on M3

Note

If you already have an M3 project, skip the next step

  1. Request a MASSIVE project as per instruction here.

  2. Pull data from XNAT to M3 use module xnat-utils (https://pypi.org/project/xnatutils/). xnat-utils is a collection of scripts for conveniently up/downloading and listing data on/from XNAT. After loading this module on M3, an additional 6 command line options are available:

module load xnat-utils  # Loading module
xnat-get    # download scans and resources from XNAT to M3.
xnat-put    # upload scans and resources (requires write privileges to project) from M3 to XNAT
xnat-ls     # list projects/subjects/sessions/scans
xnat-rename # renames an XNAT session
xnat-varget # set a metadata field (including “custom variables”)
xnat-varput # retrieve a metadata field (including “custom variables”)

The code below shows an example of pulling data from Monash-XNAT to MASSIVE M3:

# If using xnat-utils for the first time on M3, you will be prompted with
# the address of the server you would like to connect to, in addition to
# your username and password:
xnat-ls
XNAT server hostname (e.g. mbi-xnat.erc.monash.edu.au): xnat.monash.edu
XNAT username for 'xnat.monash.edu':
Password:

# To list available projects at Monash-XNAT use ‘xnat-ls’ command
xnat-ls

# To list all subjects within a specific project at Monash-XNAT
# For example: project id = 'MMH000'
xnat-ls MMH000

# To pull data from Monash-XNAT to MASSIVE M3 use the ‘xnat-get’ command
# line. You can specify project name, subject directory within a project or
# a specific sequence to download to M3.
# Use ‘xnat-get -h’ for possible options:
xnat-get MMH000

# By default xnat_get download data to your M3 project’s home directory.
# However, you can specify a path to the target by using ‘--target’ option.
# For example:
xnat-get MMH000 --target ~/'DOWNLOAD-DATA-TO-THIS-PATH'/