Managing Data

• 1: Downloading Data
• 1.1: Zip Download
• 1.2: Desktop client
• 1.3: Download Scan
• 2: Viewing Images
• 3: Uploading Data
• 3.1: Web Upload
• 3.2: Resource uploader
• 3.3: Prearchive
• 4: Syncing Data
• 5: Anonymising Data
• 5.1: Project anonymiser
• 5.2: Site anonymiser

1 - Downloading Data

1. Navigate to Scan or Session (See guide on browsing data)
2. Select Download from controls on top right.
3. Use the following settings for downloading dataset as zip

For further information refer to the XNAT official guide on downloading data

1.1 - Zip Download

The Project, Subject and Sessions page has the option to Download Images from the right hand side menu

Select Option 2: ZIP download

Filter out the Session and scans from the first two columns and select Submit

1.2 - Desktop client

The XNAT Desktop client is maintained by the XNAT development team. For information see the link below.

XNAT Desktop client

https://www.xnat.org/download/desktop-client/

Install client

Download and install the client for you operating system

Download images

The Project, Subject and Sessions page has the option to Download Images from the right hand side menu

Select Option 1: Download via Desktop Client

Click Download Via App

Select a local destination folder

Download should start, and progress can be monitored

1.3 - Download Scan

Induvidual scans can be downloaded from the Sessions page

Multiple scans can be selected and downloaded using Bulk Actions

2 - Viewing Images

XNAT OHIF Viewer

AIS XNAT instances come with the XNAT OHIF Image viewer Which is a plugin developed by the Institute for Cancer Research in London

Just note, if your publication uses the OHIF viewer, they have an article for citation. This information is all available at the link below

Documentation

https://wiki.xnat.org/documentation/xnat-ohif-viewer

Using the XNAT OHIF Viewer

https://wiki.xnat.org/documentation/xnat-ohif-viewer/using-the-xnat-ohif-viewer-122978515.html

Opening images in OHIF viewer

You can access the viewer from Session page

Just click View Image on the actions panel

This will take you to the OHIF Viewer

3 - Uploading Data

1. Web Upload (Compressed image uploader)
2. XNAT data client
3. CTP

For further information refer to the image session upload methods in XNAT

3.1 - Web Upload

Uploading DICOM datasets

1. De-identify DICOM on scanner or upload pc
2. Zip DICOM files into a zip file
3. Login to XNAT (see Login to XNAT)
4. From the top panel, select Upload → Images → Compressed Uploader

5. Specify the following options:
   • Project
   • Destination: Select Prearchive
   • Choose file to select zipped file with DICOMs

6. Click Begin Upload Wait for:
   • Upload percent bar to finish (**percent bar may not appear for small datasets)
   • Background processes panel to appear on bottom right
   • Green tick on under Upload extraction/review for archival

In case of Background process errors, expand panel using double arrows on bottom right for more details

For further information refer to the XNAT official guide on using the compressed image uploader

3.2 - Resource uploader

This is to create a web upload form for repeated uploads of any data type.

Navigate to Project → Manage → Project Resource Settings → Start

Select Image Sessions. Enter the following required fields

• Title: e.g. Rawdata
• Resource Folder: e.g. RAW
• Extract compressed files by default

Select Add when complete

To upload file(s) using the resource uploader, Upload Additional Files from the Sessions page

3.3 - Prearchive

If a dataset has not arrived into your XNAT project, the prearchive would be the place to check

This usually happens when:

• a DICOM dataset matching an existing session gets resent
• a part of a session gets uploaded separately

Accessing the prearchive

Go to Upload on the top menu, and Go to prearchive

The following is an example of a session that is in conflict. We can select the session and choose Details.

Here we can download the session, or individual scans. And review the datasets

• Choose Archive if you want the dataset merged into the existing one on the archive,
• choose Modify and Archive if any details need to be changed before archiving, or if you don’t want this dataset to merge with the existing one

4 - Syncing Data

The UQ-RCC XNAT may be able to sync datasets to other XNATs in Australia.

To see if your project is able to be synced, send a ticket to RCC support (rcc-support@uq.edu.au)

They will need the details of the XNAT that you wish to share data with.

5 - Anonymising Data

5.1 - Project anonymiser

The Project level anonymiser uses a scripting syntax called DicomEdit to modify, reassign or blank DICOM tags. You can actually use this to create automated workflow for renaming DICOM metadata on datasets

Dicomedit

https://wiki.xnat.org/xnat-tools/dicomedit/dicomedit-6-3-language-reference

version "6.1"
project != "Unassigned" ? (0008,1030) := project
(0010,0010) := subject
(0010,0020) := session

The example in this screenshot basically replicates the behaviour in the HIRF onsite anonymiser for remapping the ReferringPhysicianName, PatientName and PatientID

You can use DICOMedit to enforce a particular naming and tagging scheme across your entire project this way.

Anonymising existing sesssions

The Project level anonymiser works best for new sessions, as it runs when the dataset is being ingested into the XNAT archive, or when sessions are renamed. By default, it does not anonymise sessions that are sitting in the archive already.

If you need to trigger your anonymisation on an existing session

• Edit a session name. Modify
• Then edit it back to its original name

This will trigger the anonymisation script.

5.2 - Site anonymiser

HIRF and CAI data are anonymised on-site by default with the following protocols

Modified Tags

Blanked Tags