This includes registering for a license, which you will need to place in the FreeSurfer directory in order to use the software. When you have finished downloading and installing the package, you will use freeview to check whether the software installed successfully. We will cover more advanced features of freeview in a later tutorial. Note FreeSurfer is designed for Unix and Macintosh operating systems. It is possible that there is a way to install FreeSurfer on Windows by using a Unix emulator, but there is no systematic documentation on the FreeSurfer website demonstrating how to do it.
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AFNI, SPM, and FSL all have data viewers which basically do the same thing: the user loads imaging data, usually anatomical or functional images, and can view them in three dimensions. FreeSurfer has its own viewer called Freeview, which can by launched from the Terminal by typing freeview and pressing enter. The image can be viewed in all three dimensions in the Viewing Panel, or you can change the layout so that only one viewing dimension is displayed. The checkbox next to each image can be checked or unchecked to make the image visible or invisible, respectively.
As with the other viewers, the image at the top is the overlay - it covers all of the other images. The up and down arrows allow you to bring one particular image to the top of the stack, or to lower an image so that it is no longer the overlay image. The Opacity slider allows you to keep an image as an overlay, but to change its transparency so that you can see the image immediately underneath it.
The Toolbar is underneath the Control Panel, and it contains options for changing the opacity, contrast, and color map of the images. When an image such as aseg. Many of the images in FreeSurfer are encoded like this.
It will take some time to find out which ones are, but a useful heuristic is to assume a look-up table for any image that is segmented such as aseg. This will overlay a 3D representation of the surface in the three-dimensional box of the View window, and will trace the outline of the surface in the orthogonal boxes i.
The color of the surface in the orthogonal views can be changed by selecting a new Edge color. For example, if you wanted to create the same layout in the figure above - that is, load the orig. The colons indicate an option for the file they are attached to; for example, aseg.
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