White Matter Edits

FreeSurfer Overview

After editing control points to include white matter that was outside of the surface, you may need to edit the white matter volume itself to get rid of gray matter that is inside the surface boundary.

1. Backup. As usual, the first thing to do is backup the original white matter volume file. To do this, go to your subject's mri folder and copy wm.mgz to wm_orig.mgz:

   $ cd /path/to/subjects/directory/subjectfoldername/mri
   $ cp wm.mgz wm_orig.mgz

2. Open FreeView and load the necessary files. This part is just like opening up the files for control point edits. Open FreeView and load the orig.mgz and wm.mgz volumes from the mri folder, and the lh.white and rh.white surfaces from the surf folder. Make sure wm is above orig and change the colormap of the wm volume to heat and lower the opacity so you can see it over the orig volume. Again if you want to open the files directly from the terminal, use:

   $ cd /path/to/subjects/directory/subjectfoldername
   $ freeview -v mri/orig.mgz -v mri/wm.mgz:colormap=heat -f surf/lh.white -f surf/rh.white

   Note that you don't have to open the control points this time.

3. Erase gray matter. There will be areas in the brain where FreeSurfer thought that gray matter was white and drew the surface around it. In this case, the red/yellow wm volume will cover those gray matter areas, and we need to erase the wm volume there for FreeSurfer to get it right the next time around. On the left of the screen under the "Volumes" tab, make sure wm is selected and set "Brush value" to 0 - this will enable you to erase areas of the volume. Now look through the brain and find the areas that are actually gray matter inside the surface boundary and erase them.

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

For more about white matter edits, see the official FreeSurfer wiki.

Next step: Reconstruction Process

FreeSurfer Overview