usage: area
area is a graphical tool for the interactive viewing and measurement of magnetic resonance scan slices. The graphical user interface consists of four main areas: the image window occupying most of the screen, the message window across the top of the screen, image and view information at the top right, the histogram window at middle right, and control buttons at the lower right.
The Load Image button typically is the first command issued during an area session. This loads a Silicon Graphics RLE image and displays it in the image window. The image is magnified by the factor specified in the Magnification box in the image and view information. If the image contains sixteen or fewer distinct pixel intensities, it is assumed to be a segmented image, and no blurring is done during the magnification. Otherwise, the magnified image is blurred to prevent a blocky appearance. A normalised histogram of pixel intensities is displayed in the histogram window. The image label is set to the name of the image file.
If the name of the image contains a digit string, and files exist in the same directory whose names are the same as the name of the current image except that the corresponding digit string represents the next or the previous integer, then the Next Image and Previous Image buttons, respectively, are displayed. In the case of image names that contain more than one separate digit string, the leftmost digit string is used for this substitution. These buttons function analogously to the Load Image button.
When an image has been loaded, the Load Tracing button appears. This button loads and displays a tracing that has been saved as a greyscale Silicon Graphics RLE image.
Tracings are created using the mouse. The left mouse button writes a freehand drawing on the image. The middle mouse button is used to draw straight lines; press it at one endpoint and release it at the other. To erase an N-by-N square surrounding the mouse cursor, press the left and middle mouse buttons together. When the size of the magnified image is larger than the size of the image window, the right mouse button drags the visible portion of the image within the window.
When a tracing has been loaded or drawn, the Save Tracing and Clear Tracing buttons appear. These are used to save the current tracing as a greyscale Silicon Graphics RLE image and to erase entirely the current tracing, respectively. There are also Next Tracing and Previous Tracing buttons whose functions for tracings are analogous to the functions of the Next Image and Previous Image buttons for images.
The Measure button measures a closed area defined by the current tracing. After clicking the Measure button, the message window prompts the user to click the left mouse button within the region to be measured. After some preliminary processing which may take a few moments, the program begins to fill the region with the tracing colour. Once the region is completely filled, the display is frozen for one second and then reverts to the original tracing. Measurements are displayed in the image and view information area. Which measurements are displayed depends on the type of the current image. Total area of the region of interest is always displayed. If the image is segmented, area for each numeric tissue category is displayed. (The tissue categories are coded only as numbers, and are computed dynamically when the image is loaded, so this method is compatible with any numeric coding of tissue categories.) If the image is not segmented, the mean, median, and modal pixel intensities within the region of interest are displayed. These measures include all the tissue within the traced boundaries, but not the areas occupied by the boundary lines themselves.
The Save Measurement button exports the currently selected measurements to the current measurement data file. The measurements are exported as ASCII text separated by commas, suitable for importing into a spreadsheet program. Measurements can be selected and deselected by clicking on them; a light next to a measurement indicates that it's selected. If no measurement data file has been selected, the user will be prompted to select one as if the Select Measurement Data File button had been pressed.
If the environment variable HOME is set, settings are saved between one area session and the next in the preferences file $HOME/.area. The format of this file is as follows:
HFOV VFOV ZOOM Image Directory Tracing Directory Measurement Directory Measurement Data File
Author: Matthew Belmonte. Based on a problem definition by Stuart Hinds and Brian Egaas. Uses the XForms library by T.C. Zhao and Mark Overmars.