This short minute course was held at RSNA in Chicago on Nov 28 and Dec 1, The course offered a brief introduction to main. Segmentation steps using ITK SNAP semi-automatic segmentation based on Intensity Regions. From left to right, top: Definition of the region of interest.

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ITK-SNAP tutorial available online | PICSL

In this tutorial, automatic segmentations were initialized using ‘bubbles’. The gains in speed come, of course, at the price of accuracy. When you are satisfied with the feature image, press Okay to compute the feature image at all voxels and close the intensity region filter window.

These velocities are displayed using a fixed feature image, and not wnap feature image that you are working with. It is up to the user to come up with the list of labels to use in a particular segmentation task.

How is This Tutorial Organized? If the selection box disappears in one of the slice windows, tutoril means that the crosshairs position is outside of the selection box.

What Additional Documentation is Available?

In this tutorial, we will use the term grey image to refer to the three-dimensional input image, e. The experimental noise reduction option can be used in conjunction with overriding the optimal time step.

The Dense Level Set Algorithm is included purely for experimental purposes. Simply select this tool, position the mouse over a rendered segmentation results e. You can, however, follow the general directions of this section using a different image, but you will have to use your own judgement in selecting various parameters. Next igk the step size dropbox is a display that shows the current iteration.


This window consists of two parts.

SNAP Tutorial and User’s Manual

In order to ittk the scalpel tool, we need to first rotate the 3D view such that a line can be drawn between the two caudates. Otherwise, press the Accept button to repaint one of the caudates with the active drawing label and press the Update Mesh to see the result in 3D.

In this step we will construct a region competition feature image appropriate for segmenting the caudate nuclei. At the top of the control panel is located a menu barwhich is used for saving and loading images, for setting options, and for accessing the help system.

Click below to jump to a specific tip:. SnAP lets you save and load ltk images. You will need to use the Above threshold direction setting when creating the feature image. After you use the mouse to click on and move the knobs that are used to change the threshold and smoothness values, you can use the left and right arrow keys to move these knobs one value at a time.

This tab allows you to change the algorithm used for snake propagation.

Tutorial: Getting Started with ITK-SnAP

Before starting automatic segmentation, create a manual segmentation as described in Section 4 using the same label that you wish to use for snake segmentation. The crosshair position can be adjusted in this mode using the left mouse button as usual. Move the mouse around the 3D window. We will see how to use the control panel in the subsequent sections. The Snake Parameters window is shown below.


If your input device does not have a right anap a middle mouse button, use the tik combinations keyboard mouse combinations: Whenever you enter the automatic segmentation mode with some label X as the current drawing label, all the pixels already labelled X will be passed on to the automatic segmentation mode as initialization pixels.

However, you can use subsampling to get a ‘quick and dirty’ segmentation and then use that segmentation as an initialization to another segmentation, this time without resampling. First and foremost, SNAP was designed for clinical users. The second is used to enter the automatic segmentaiton mode of SNAP. Use the Radius slider to change the radius of the bubble. Under each of these panels are located several blue buttons, which are used to interact with each panel individually.

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