Working with FIV

Depending on your mode settings and the command line options you use (see below), when FIV starts, you’ll see a view of your images and/or the FIV toolbar (Fig. 1). If the toolbar isn’t visible, click in the image window and type Ctl-t to open it.

Fig. 1 The FIV toolbar

The upper left panel includes components to open a view of your image. Use the dropdown boxes to the right of the 'Go' button to select the slice orientation and display type, and then click 'Go' to bring up the view. The 'montage' display presents a subset of the slices in a tiled format similar to xds, and the 'stack' display presents the individual slices in your image in a scrollable stack (Fig. 2).

Fig. 2 A montage window (left) showing a transverse view and a stack window (right) showing a coronal view.

The upper right panel shows the current activation and structural files and provides buttons for selecting different files. If you point the mouse over one the file names and hit the space bar, the complete path of the file will appear in a popup window.

The bottom left panel of the toolbar provides buttons to access various tasks and manipulations:

	Saves the current image window as it appears as a .gif file.
	Prints the current image window as it appears.
	Opens the preferences/modes dialog.
	Opens the information and error log window.
	Sets current and subsequent windows to synced mode. Windows in sync mode are affected by various manipulations, including adjustments to activation range, which usually affect only the current window. Also, mouse motion and clicks within an image window are tracked by the crosshairs and displayed slice in synced stack windows. At startup, FIV is in synced mode.
	Toggles visibility of the ImageJ window. The ImageJ window includes additional tools for analyzing your images. Some of the functionality of ImageJ is not currently operable within FIV.
	Toggles the visibility of the crosshairs.
	Toggles whether subsequent windows are displayed in radiologic orientation (left hemisphere on the right.) Current windows are not affected. A small green letter at the bottom of each window indicates its orientation.
	When depressed, contrast and brightness of the structural image can be adjusted by dragging the mouse in the image window or with the arrow keys.

The lower middle panel on the toolbar is used to specify the range of activation values that is displayed in the current window(s) and subsequent windows. You can specify whether positive and/or negative activations are displayed using the dropdown box. FIV is agnostic as to what type of data is stored in the activation file you give it, so you should use threshold values that are appropriate to the statistic that is represented in the file. Typically, you'll want to use files containing z-values or -log p values.

The lower right panel displays the Talairach coordinates and activation values in your images. To update the display to the values at the current mouse position, click the left mouse button. Alternatively, if you type Control-B the values will update continuously as the mouse moves through an image window. Also, you can press the space bar to get a popup display of the values at the current mouse position. You can also type coordinates into the coordinate boxes in the toolbar window to obtain the activation value at the specified coordinate and to move the crosshairs and displayed slice in the stack windows.