Control Point Edits

FreeSurfer Overview

As you did for skullstripping, SSH into the computer you'll be working from (again you'll probably want ba8) by entering into the terminal:

$ ssh -X <username>@ba8.mit.edu

Open up FreeView:

$ freeview &

Now go to FreeView and you can start making control point edits:

On the left, you will see 3 tabs (Volumes, Surfaces, Point Sets) like this:

Loading the Necessary Files

1. Volumes

   • Click on under the "Volumes" tab and go to the folder that contains the MRI volumes (usually called mri). Load orig.mgz and wm.mgz onto FreeView.
   • For wm.mgz change the Color map from "Grayscale" to "Heat". Make sure that the wm volume is above the orig volume.
   • Play with the opacity of the wm volume until you see white/gray matter contrast.

2. Surfaces

   • Now go under the "Surfaces" tab and click on the icon with the green '+'. This time, go to the folder that contains the surfaces (it's usually called surf). Load lh.white and rh.white.

3. Point Sets
   This is essential to adding control points.

   • If this is your first time adding control points to this brain, click on to create a new control point set. Name the new point set control.dat, make sure you select "control points" instead of "way points", assign template volume to wm, then click "OK".
     
   • If you have previously made a point set for this brain before, click on to load control.dat from the tmp folder (this should be in the subject folder). Again make sure you select "control points" instead of "way points".

Note. Loading the above files can be done entirely from the terminal if you're interested:

$ cd /path/to/subjects/directory/subjectfoldername
$ freeview -v mri/orig.mgz -v mri/wm.mgz -f surf/lh.white -f surf/rh.white -c tmp/control.dat &

Adding Control Points

Click on to change your cursor to a point set editor. Now you can add control points to the wm volume. Control points are used to include white matter that is not inside the surface - if there's a large area, just put a lot of control points there. Don't try to use control points to get rid of gray matter inside the surface boundary, that's what white matter editing is for.

Applying Control Point Edits

When you're done, put the brain on the queue on ba3 (see Reconstruction Process).

Helpful Shortcuts

• PageUp and PageDown are used to go up and down the brain.

• Ctrl+Z works the way you think it does! It's the undo button.

• Click on a control point while pressing Shift to delete an individual point.
  You may find it helpful to toggle (check/uncheck volumes and surfaces) in order to see exactly where the white matter/gray matter boundary is.

• Ctrl+V allows volume toggling

• Ctrl+F allows surface toggling

• Ctrl+C allows toggling between the two surfaces (make sure you are under surfaces tab to use this one)

• See the official FreeView wiki for more shortcuts

Next step: Reconstruction Process

FreeSurfer Overview