Freeview

Loading Volumes, and Surfaces

Freeview allows users to edit the white matter volume (wm.mgz) as well as make pial edits to the brainmask.mgz volume. The voxel edit tool in freeview allows the user to make edits to whichever volume they desire. First open freeview by typing <freeview> into your terminal. Now select volumes on the control panel and load wm.mgz and brainmask.mgz. Select and highlight the wm.mgz volume and configure the settings as follows, color map:heat, opacity:.40, min:0, mid:125, max:225, offset:0, and Brush value: 255. Alt + c toggles which volume you are looking at. Ctrl + mouse-wheel changes slides. Now that the volumes have been loaded into the control panel you must now load four different surfaces into freeview, the lh.pial, lh.white, rh.pial, and rh.white. The edge colors will be set to yellow as a default. It is a good idea to change the edge colors of one of the surfaces in both hemispheres to differentiate between the white matter and pial surfaces.

Voxel Edit

The next step after setting up the volumes and surfaces is configuring voxel edit. Voxel edit can be found in the control panel. This will bring you to a window that has all of the tools freeview has to offer. The tool we will be using is freehand, which is the tool on the top left of the edit window. To edit the wm.mgz volume set the brush size to 1, or 2. The brush value to 255, and make sure the reference is wm.mgz. You can now add in white matter voxels by left clicking, and delete voxels in the white matter volume by shift + left click. Pial edits in freeview must be done with the brainmask.mgz volume highlighted in the control panel. Now reference the brainmask.mgz volume in the voxel edit window. Left click will now add pial while shift + left click will delete voxels from the volume.

Identifying Areas to Edit

Now that we know how to edit the volumes, it is important to be able to identify where edits are needed. The best way to do this is to open tksurfer. You will notice in the inflated, and pial surface if there are any peaks or valleys. Moving your cursor over one of these points of interest and clicking it will bring up a vertex index under cursor. You can now save the point that you have just identified. Now in freeview, go to tools>go to saved point. This will bring your cursor in freeview to the vertex that you identified in tksurfer. When you go to the saved point in freeview the cursor will move to the part of the brain you identified as suspicious in tksurfer, but does not go to the specific slide that may need editing. flipping through the slides and using the saved point as a reference saves a lot of time in identifying areas that need edits.