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Quick Start

Freeview is started by invoking it from the command line. The user must first source the developmental (updated regularly) version of Freesurfer by opening a terminal window and typing (or copy-pasting) this command:

source  /usr/local/freesurfer/nmr-dev-env

The user must next navigate to the directory in which the volume is saved in order to open it. Example:

cd /autofs/space/rainbow_002/users/hires/FHS19_ec_amyg_032808/mri/flash

Be sure to type the command sp in order to set this directory as the one in which to save changes and/or new volumes. After that, open the desired volume using the command:

freeview -v volumename.mgz

After loading the inital volume, other volumes can either be added or loaded from the open Freeview window.

To load a new volume: Go to File>New Volume or click the new volume icon on the toolbar. Enter the name of the new volume in the standardized format, and make sure the selected template volume is the original volume.

To open a previously saved volume: Go to File>Load Volume, press Ctrl+O, or click the load volume icon on the toolbar. The correct volume may be selected to open by navigating through the directory in the Load Volume dialogue box. Select the desired saved volume, and hit "OK."

You can explore data in a number of different viewing fields, and orientations. To see all orientations at once, including the 3D representation, choose from the toolbar on the top either 2x2 (pic), 1&3 (pic), 1&3 horizontal (pic). To have one orientation as full screen, choose the 1x1 option (pic). To the right of these buttons are the buttons with which you can change the orientation: saggital (pic), coronal (pic), axial (pic), and 3D (pic).

You can move through the data using the mouse. Clicking on the data at a certain point will move the red crosshair to that point (as long as you are in Navigate mode, see below), the coordinates of which will be given on the bottom of the window. To scroll through slices, use Page Up and Page Down on the keyboard. To zoom in and out, use the scroll button on the mouse. To move the whole image, either click and drag using the scroll button on the mouse, or use the arrow keys on the keyboard.

In the top, left corner of the window, directly beneath the File and Edit menus you can switch between Navigate (pic) and Voxel Edit (pic) modes. While in Navigate mode, you can use the mouse to move the red crosshairs and navigate through the data. Click to Voxel Edit mode, a drawing toolbox appears, and you can draw upon the volume. In the lefthand control panel, you can change Color Maps, adjust the opacity (useful when working with multiple volumes in the same window), and adjust the contrast (Window, Level, Min and Max sliding bars).