3D Slicer

Getting 3D Slicer

Download the latest stable release of 3D Slicer from the Slicer site. It has an open-source licence. Install the software. For example, under MS Windows 7, just run the downloaded executable file (e.g., Slicer-4.4.0-win-amd64.exe).

The Web site includes good documentation and tutorials, although it is sometimes hard to find details about simple things. There are over 100 modules to choose from for various kinds of operations. The discussion forum is quite active and the developers are responsive. On 2017 Apr 7 a new Slicer forum was opened at discourse.slicer.org; as of 2017 Jun 8, users posting questions on the old slicer-users e-mail list are asked to repost their questions on the new forum, but the instructions on the Slicer Web site are still to use the e-mail list.

They don't seem to be able to decide whether the programme is called 3D Slicer, 3DSlicer or just Slicer.

If you get an error message, you can see the details in the error log by clicking on the error-log icon Error-log icon in the lower-right corner of the Slicer window, or by selecting View ► Error Log. The message texts may disappear off the edge of the error-log window but you can see the full text of a message by clicking on it.

Simple exercise

Loading sample data

Do File ► Download Sample Data (or select Download Sample Data in the initial Welcome module) and select one of the datasets.

Slicer can load sets of JPEG images but I haven't figured out how to set the pixel size and slice spacing. The software would take forever (approximately) to load a set of, for example, 700 images of 1024×1024 pixels.

DICOM is a format that is commonly used for medical imaging.

3-D rotation is awkward because there is no z rotation, except clumsily with a button in the module View Controllers.

Viewing the data

In the default display layout, three orthogonal slices through the image volume are displayed in three separate panels. A fourth panel is a 3-D view. To display the slices in that view as well, within each 2-D panel hover with the mouse over the tiny push-pin icon push-pin icon in the upper left corner of the panel and, in the set of icons that pops up, click on the closed-eyelid icon Closed-eye icon. It turns into an open eye Open-eye icon and the image slice appears in the 3-D panel.

Doing segmentation

From the dropdown list of modules on the toolbar, select Segmentation ► Simple Region Growing Segmentation.

To create a seed point for the algorithm, click on the arrow-and-red-blob ‘Fiducial’ icon Fiducial icon and then click on a location in the image. (The icon is confusingly described as ‘an arrow pointing to a sphere fiducial’ – the arrow points away from the red blob, and ‘fiducial points’ normally refers to markers used for alignment, not to seed points.) A numbered marker will be displayed at the location.

When a first seed point is created, it is added to a new list of seed points, obscurely named F. In the Segmentation Parameters panel, click on the Seeds dropdown list and select F as the current list of seeds.

In the IO panel, click on the Input Volume dropdown list and select the name of the dataset that you are using. Then click on the Output Volume dropdown list and select Create new Volume.

Click on Apply. If you're lucky, there will be a few seconds of processing and then the segmented region will be highlighted in the displayed images.

If the segmentation doesn’t include enough, you can define additional seed points by repeatedly clicking on the icon and then clicking in the images. Alternatively, you can click on the small triangle beside the icon and select Persistent in the drop-down list – if the Persistent attribute has a checkmark beside it, you can click once on the arrow-and-blob icon and then click repeatedly in the images to create multiple seed points.

You can use the Markups module to edit the list of seed points, removing some if you got too much or adding some if you didn't get enough.

You can also increase or decrease the amount included in the segmented region by increasing or decreasing

See the documentation for more information.

Creating surface model from segmentation

Select the module Surface Models ► Model Maker. In the IO section make sure the ‘volume’ corresponding to your segmentation is selected as the Input Volume. For Models select Create new ModelHierarchy. Make sure the Generate All Models box is checked (or specify the labels in the Model Maker Parameters section). Click on Apply. If you're lucky, after some processing a 3-D surface model will appear in the 3-D section of the display. Note that there are a lot of parameters that can be played with in an attempt to improve the model, with varying degrees of loss of control.

To switch between perspective and orthographic views of the model, hover with the mouse over the tiny push-pin icon in the upper left corner of the panel and, in the set of icons that pops up, alternate between the perspective Perspective-view icon and orthographic Orthographic-view icon icons.

Slicer doesn't seem to be able to export the model in VRML format.

Volume rendering

The module Volume Rendering can be fun to play with. Select the desired Volume and make sure the eye icon beside the Volume: selector is open. There are many many parameters that can be adjusted, as well as some preset sets of settings like CT-Bones and MR-Angio. For example, try the CTChest sample data with the CT-Bone preset. The 3-D images are impressive at first glance but actually contain a lot of junk.

Note that this volume rendering has nothing to do with the results of the segmentation above.

Saving results

Use File ► Save to save things like lists of region-growing seed points and results of segmentations. The default location for saved files is the directory where the Slicer programme itself is located, which is a bad place to save things. The Change directory for selected files button in the Save dialogue can be used to change the directories for all of the file types at once.

Other tasks

Slicer has tools for many other tasks, including image filtering, registration and quantification, and specialized applications like image-guided therapy and endoscopy. These tools are ‘for research purposes only’ and have not been approved for clinical use.


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R. Funnell
Last modified: 2018-03-10 11:29:32