Freesurfer Quality Control Guide

Step 1: Correct the Pial Surfaces to remove any non-brain tissue

Step 1a: 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/brainmask.mgz:colormap=jet:colorscale=0,1:opacity=0.3 \
-f $SUBJECTS_DIR/$SUBJ/surf/lh.pial:edgecolor='255,0,0' \
-f $SUBJECTS_DIR/$SUBJ/surf/rh.pial:edgecolor='255,0,0' &

Step 1b: -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
  • brainmask.mgz



Load the following surface files for that subject:

  • lh.pial
  • rh.pial



Adjust the colors of the volumes and surfaces so you can see the types of errors best. For example, for brainmask.mgz, select the “Jet” color scale with the minimum as 0, max as 1. Set the opacity to 0.3. For the pial surfaces, choose a color with good contrast like red or blue.

Step 1c: Locate non-brain tissue inside the pial surface

When you are looking for non-brain tissue in the pial surface, the best view to use is often the coronal view. Additionally, it is helpful to turn the various layers (pial surfaces and brainmask volume) on and off, so you can compare them against the anatomy in orig.mgz when deciding whether the boundaries are correct or need editing.

In the figure below, note that some non-brain tissue is inside the pial surface in the space between the inferior frontal lobe and the temporal pole. This non-brain tissue has been included in the pial surface on the inferior frontal side. This mistake occurs bilaterally.

If it’s off, turn on the layer associated with brainmask.mgz

Select the “Voxel Edit” tool.

Set the brush value to “0“.

Paint the areas of brainmask.mgz that are incorrectly included within the pial surface. Be careful to make sure “brainmask.mgz” is selected (highlighted) in your list of volumes!

When you have corrected the defects, save the brainmask.mgz volume

Two common places for these defects to occur are around the eyes (as in the images above) and in superior areas with bright dura (as in the picture below).

Step 1d: 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 -autorecon3 -subjid $SUBJ

… where $SUBJ is the subject identifier. Re-processing the brain will take approximately 8 hours on the lab terminals. Use this time to work on another brain!

Next: Go to Step 2