Viewing images on UKB RAP with 3D Slicer

Find 3D Slicer in the list of available tools.

Note the version of 3D Slicer and Click Run to set up the inputs to the tool.

Files can be selected within <Input files> using the browser. Alternatively, a Manifest of Input Files can be provided. In this case, do not provide input to <Input files>.

The file format should consist of list of file IDs, one per line, in <project ID>:<file ID>. 
For example:

project-AbCdE12F34G:file-HI12JK34LM56OP
project-AbCdE12F34G:file-QR12ST34UV56WX

Files specified in the Input Files and Manifest of input Files start up parameters can be mounted to the 3D Slicer application (rather than downloading as part of the application start up process). 

This can enable the user to reduce the size of the instance for running the application.

After starting the application, the instance will take some time to change to status "Running" at which point it will be possible to "Open Worker URL", at first you are likely to experience a "502 Bad Gateway" error. This is presented while the compute is downloading and installing the necessary components. After successful installation and set up the standard 3D Slicer interface should be presented on a browser refresh (Note, installation and setup time will depend on compute instance used).

File and UKB-RAP project management within 3D Slicer

Activating the button with the DNAnexus logo on the taskbar will display the DNAnexus File Manager extension shown below. Using this extension, it is possible to view files in the local compute file system, including downloaded and mounted image files. Files can also be selected and uploaded back to your UKB-RAP project.

Viewing Non-DICOM (e.g., NIFTI) Images

After inclusion in the Input Files or Manifest of input Files, NIFTI (.nii) image files can be extracted and imported from zip archives.

Then click Choose File(s) to Add. 

Then select the file(s) specified in the Input Files or Manifest of input Files input parameters. After clicking OK, 3D Slicer should then attempt to load all images.

Viewable images/volumes are displayed with a (small) cube. When volumes/images are not selected for visibility, an empty circle accompanies the cube. When selected for visibility in the viewing frames, an eye is shown with the cube. See the green highlighted symbol on the T1 line in the example below. This symbol can be toggled to update the image in the viewing panes. The example below shows the data in an extracted T1 FreeSurfer output folder (some of these data are in .mgz format and these also import successfully).

- This symbol is presented on the toolbar and reveals the Subject hierarchy view.

Only a single image volume can be selected at once, in the case above, toggling the eye symbol on the wm volume will hide the T1 volume. However, overlays can be applied. These are displayed with a green face on the cube on the left side. In the case of the Scene list above, the wm.seg LabelMapVolume has dimensions that match the T1 image. In this case, the overlay can be applied to the volume and visualised at the same time. 

Viewing DICOM images

After including DICOM images in the <Input files> or <Manifest of input Files> parameters, the DCM ZIP module on the toolbar will allow you to select zip archives.

Selecting zip archives that contain DICOM files, e.g., field 20201 - neck-to-knee MRI scans, and selecting Open will preload the DICOM data into the 3D Slicer DICOM database. Note this method cannot be used to load non-DICOM data.

After opening the DICOM files in the database, the imaging identifier will be provided in the Patient name and Patient ID columns of the upper window, the acquisition date will be presented in the centre window, and details of the available DICOM series will be presented in the lower window. Selections of participants, studies, and specific series can then be made before clicking Load to then allow images to be viewed.

The side pane on the left hand side will then show a nested view of participant, study, and series data. 

As with selecting NIFTI series to view (see Viewing Non-DICOM (e.g., NIFTI) Images section), the small eye symbols can be left clicked to toggle visibility.

3-dimensional renderings can also be generated by right clicking the eye symbol and selecting Render in 3D visualisation.

Further built in 3D Slicer visualisations

• 3D volume rendering - higher instance CPU requirements
• Transformations