Download the latest stable release of
3D Slicer from the
It has an open-source licence.
Install the software.
For example, under MS Windows 10, download and run the
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.
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 in the lower-right corner of the Slicer window, or by selecting. 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.
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 it is not possible to rotate the scene around an axis perpendicular to the screen.
Do(or select in the module) and select one of the datasets.
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 in the upper left corner of the panel and, in the set of icons that pops up, click on the closed-eyelid icon . It turns into an open eye and the image slice appears in the 3-D panel.
From the dropdown list of modules on the toolbar, select.
To create a seed point for the algorithm, click on the arrow-and-red-blob ‘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
the panel, click on
the dropdown list and
select as the current list of seeds.
In thepanel, click on the dropdown list and select the name of the dataset that you are using. Then click on the dropdown list and select .
Click on. 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 selectin the drop-down list – if the 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 themodule 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.
Select the module. In the section make sure the ‘volume’ corresponding to your segmentation is selected as the . For select . Make sure the box is checked (or specify the labels in the section). Click on . 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 and orthographic icons.
Slicer doesn't seem to be able to export the model in VRML format.
The modulecan be fun to play with. Select the desired Volume and make sure the eye icon beside the selector is open. There are many many parameters that can be adjusted, as well as some preset sets of settings like and . 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.
Useto 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 button in the dialogue can be used to change the directories for all of the file types at once.
Slicer has tools for many other tasks, including image filtering, registration and quantification, mesh generation, and specialized applications like image-guided therapy and endoscopy. These tools are ‘for research purposes only’ and have not been approved for clinical use.