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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¶
Register a new account on Monash-XNAT.
You will receive an email to verify your email address.
3. After veryfing your email, wait for a Monash-XNAT administrator to enable your account before you can log in. Please email firstname.lastname@example.org if your account is not enabled after the next working day.
Request to create a project at Monash-XNAT¶
- Please fill out the Monash-XNAT Project Request Form:
This form is designed to collect the information needed for creating a new project on Monash XNAT instance. 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.
Monash-XNAT administrator will review it and email you to confirm the project registration.
Mirroring data from Alfred-XNAT to Monash-XNAT¶
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.
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.
The whole process cost will be calculated by the Alfred radiology team for your information.
- 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
- Create an account at Monash-XNAT NOTE:
Not needed if you already have Monash-XNAT account.
- Request to create a project at Monash-XNAT NOTE:
Not needed if you already have a project for this research at Monash-XNAT
Since Alfred-XNAT is within a firewall, Alfred team needs to 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.
Pulling Data from Monash-XNAT to MASSIVE M3¶
The steps to download data from Monash-XNAT to MASSIVE M3 are:
- Create an account on M3 Note:
Not needed if you already have an M3 account.
- Request a MASSIVE project as per instruction here. Note:
Not needed for the research project that is already allocated on MASSIVE.
Pull data from XNAT to M3 use module
xnat-utilsis a collection of scripts for conveniently up/downloading and listing data on/from XNAT. After loading this module on M3, an additional 6 command lines 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 (ex. 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 it 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'/