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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This section explains the purpose of the SNAP tool, and describes the screen layout. This section is organized as a series of questions and answers about the general capabilities and structure of the SNAP tool.
For brevity, only the most basic questions are answered here; more questions will be answered in later sections of the tutorial.
This tutorial is a walk-through of a SNAP segmentation session. The information presented in this tutorial falls into the following categories:.
The SNAP self-installer is available for download at http: Obtaining, building and running SNAP as part of this distribution requires considerable knowledge of system administration and computer programming. The directions on obtaining and installing SNAP are available at http: If SNAP has been installed on your system, consult your system administrator for instructions on starting it.
SNAP provides a set of tools to make segmentation of gutorial data easier and faster. SNAP can be used in two different modes: The manual mode is used for segmentation using hand contouring and for cleaning up the results of automatic segmentation.
In the semi-automatic mode, a powerful level set segmentation algorithm is used to segment anatomical structures in three dimensions. This algorithm requires some guidance from the user, and SNAP provides itkk easy interface to provide such guidance.
First and foremost, SNAP was designed for clinical users. A user who already uses a computer for image segmentation, and thus understands the fundamentals of three-dimensional medical imaging will be able to use SNAP after completing this tutorial. SNAP does not require a deep understanding of the underlying mathematics and computer science to use.
SNAP user interface also provides some controls designed specifically for tutirial userswho are familiar with the level set algorithms.
In this tutorial, some sections are written for the expert users, and are optional. SNAP can be used to segment a variety of three-dimensional images. The images have to be homogeneous, i. SNAP represents segmentation by assigning labels to pixels voxels in the input image. For instance, when segmenting a brain MRI, some of the pixels in the image tutoriwl be assigned the label ‘grey matter’, others will be assigned the label ‘lateral vetricle’, etc.
It is up to the user to come up with the list of labels to use in a particular segmentation task. Each voxel in the input image can only be assigned a single label. The output of SNAP is a volumetric image of labels. In this tutorial, we will use the term grey image to refer to the three-dimensional input image, e.
We will use the term label image to refer to the corresponding three-dimensional volume of labels. Since SNAP can only assign a single label to each pixel in the grey image, it can not be used for segmentation with sub-voxel accuracy.
Most of the SNAP window is occupied by four panels, three of which show orthogonal slices through an tutoroal, and the fourth, located at bottom left, shows the three-dimensional view of the segmentation. This tutorial will refer to these panels as slice panels and the 3D panel.
Under each of these panels are located several blue buttons, which are used to interact with each panel individually. The left portion of the SNAP window is occupied by a tall thin area called the control panel. At sjap 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.
The rest of the control panel houses a variety of buttons, sliders and other controls, which appear and disappear depending on the current mode of operation. We will see how tuyorial use the control panel in the subsequent sections. In addition to the main window shown above, several other windows will pop-up during the SNAP session.
These windows are used to coordinate specific tasks, such as loading and saving images, or selecting parameters in the semi-automatic segmentation mode. SNAP requires the use of a mouse, trackball, or an equivalent input device. A three-button mouse with a scroll wheel is preferred, but is not necessary. If your input device does not have a right or a middle mouse button, use the following combinations keyboard mouse combinations:.
See the list of publications at http: How is This Tutorial Organized?
Tutorial: Getting Started with ITK-SnAP
The information presented in this tutorial falls into the following categories: This is information about SNAP that is necessary in order to use the tool. Most of the text in the tutorial falls into this category.
Action items denoted by icon. These are actions that the user should perform in the course of the tutorial, such as clicking on buttons and entering text. Tips and tricks denoted by icon. This is extra information that can increase your productivity when using the tool but is not essential. Information for experts denoted by icon. This is additional, often mathematical information for advanced users.
The picture below shows the SNAP user interface in manual segmentation mode. If your input device does not have a right or a middle mouse button, use the following combinations keyboard mouse combinations: What Additional Documentation is Available?