This is accessed through File->Export->Screenshot Series menu. In addition, you can create an animation by stepping through the slices in one of the slice panels and saving a screenshot for each slice. The same functionality is also accessible through the File->Export->Screenshot menu. Screenshots generated by the camera button include all of the overlays and appearance elements in the slice panel i.e., the cursor, anatomical labels, etc. The filename is generated automatically (snap0001.png), with the number incremented each time you save a screenshot. In the upper right corner of each slice panel (and on the lower right of the 3D view panel), there is a small 'camera' button ( ) that takes a snapshot of that panel. Several options are available for saving screenshots in ITK-SNAP.
#Mac paintbrush flipping image code#
However, when you reorient the image, you must select a 3-letter code it is not possible to edit the NIfTI matrix directly. For these images, the 3-letter code closest to the orientation encoded in the NIfTI matrix is displayed (see below).
Some images are acquired obliquely and have more complex NIfTI matrices. To correspond to a letter code, the 3x3 matrix must have a simple form: a permutation of a diagonal matrix. Each code corresponds to the upper left 3x3 submatrix of the NIfTI matrix. For example, the ASL orientation has sagittal slices, and RAS has axial slices. Lastly, a graphical representation of the three-letter code is given. The actual matrix mapping the voxel coordinates to NIfTI physical coordinates is given underneath. For example ASL means that the voxel x coordinate runs from anterior to posterior, and so on. Below the codes, the explanation of the code is given. For example, above, we are changing the orientation from ASL to RAS. The reorient image dialog shown above allows you to change image orientation by changing a three-letter orientation code. By default, color maps are discontinuous at 0 and 1 and continuous at all other control points. A color map with discontinuities is illustrated below. When you do so, you can edit just one side of the control point, creating a discontinuity in color, alpha or both. To make a control point discontinuous, change the Side drop down from Both to Left or Right. The color is interpolated between the control points, and shown in the background of the graphical display.Įach control point can be continuous or discontinuous. In addition, each control point has a color, which you can change using the color chooser provided. You can change the alpha mapping by moving the control points up and down (changing their alpha value), as well as left and right (changing their color index). We want to be able to make these values transparent, e.g., when displaying statistical maps or other types of overlays. Why do we explicitly define the opacity for color index values below 0 and above 1? This is important because some intensity values in the image may be mapped outside of the range by the intensity contrast curve. Values of color index below zero (first control point) have zero alpha (fully transparent) values between 0 and 0.35 (third control point) are semi-transparent values from 0.35 to 1 are fully opaque and values greater than 1 are fully transparent.
The bold black line gives the mapping from the input range to alpha. The vertical axis is the alpha (i.e., opacity) value. Think of this display as a graph, with the horizontal axis representing the input range. Let us examine the graphical display at the top of the color map editor closely. This approach allows you to reuse the same color map for many images. The color map then maps the color index to RGBA values. Note that both the image contrast mapping and the color map are used together to determine the mapping from input image intensities to RGBA space! The intensity contrast curve maps input intensities to the color index. These last two settings may be disabled permanently by going to Tools->Display Options->General and deselecting the corresponding checkboxes. Select the zoom/pan tool (press 2) and deselect Multisession Zoom and Multisession Pan. You can also disable synchronized zooming and panning, that is on by default. Select the crosshairs tool (press 1) and deselect Multisession Cursor. You can turn off cursor synchronization if you want the cursor in each ITK-SNAP version to operate independently. However, each image is rendered in its native voxel space - there is no interpolation or resampling! As you can see, the cursor points to the same anatomical coordinate in both images. The MP-RAGE image is sagittal, and the T2 image is oriented with slices approximately orthogonal to the long axis of the hippocampus. One (in the front) is displaying an 7 Tesla MP-RAGE image, and the one in the back is displaying a T2-weighted image from the same session. The image above shows two sessions of ITK-SNAP.
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