Freesurfer Quality Control Guide

Step 3: Correct the White Matter surfaces to remove any grey matter tissue

Step 3a: Load the target subject into FreeView using the terminal:

You can also open FreeView with all the appropriate files preloaded using the following commands:

export SUBJ=YourSubjectName
freeview \
-v $SUBJECTS_DIR/$SUBJ/mri/orig.mgz \
-v $SUBJECTS_DIR/$SUBJ/mri/wm.mgz:colormap=heat:opacity=0.1 \
-f $SUBJECTS_DIR/$SUBJ/surf/lh.white:edgecolor='0,0,0':edgethickness=1 \
-f $SUBJECTS_DIR/$SUBJ/surf/rh.white:edgecolor='0,0,0':edgethickness=1 &

Step 3b: -OR- Load the target subject into FreeView using the GUI:

In your terminal, open FreeView:

freeview &

Load the following volume files for the subject you are editing:

  • orig.mgz
  • wm.mgz



Load the following surface files for that subject:

  • lh.white
  • rh.white



Adjust the colors of the surfaces so you can see white matter errors best. For example, For the white matter surfaces, we usually choose a color with good contrast like blue.

Step 3c: Edit the white matter volume to remove any non-white-matter tissue it includes.

More info on how to do this coming soon!

NB: When you are erasing white matter in wm.mgz, use a brush value of 1.  When you are painting white matter in wm.mgz, use a brush value of 255. Do not use a brush value of 0 for erasing, because the changes will not be preserved when you re-run the recon.

Step 3d: Re-process the brain

Now have FreeSurfer re-run the reconstruction, taking your brainmask edits into account. Enter the following command into the terminal:

recon-all -autorecon2-wm -autorecon3 -subjid $SUBJ

… where $SUBJ is the subject identifier. NB: This is a different command than the one used in Steps 1 or 2! Re-processing the brain for Step 3 will take approximately 3-5 hours on the lab terminals. Use this time to work on another brain!