Freesurfer Quality Control Guide

Step 2: Correct the White Matter surfaces to include any missing white matter

Step 2a: 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 \
-f $SUBJECTS_DIR/$SUBJ/surf/lh.white:edgecolor='0,0,255' \
-f $SUBJECTS_DIR/$SUBJ/surf/rh.white:edgecolor='0,0,255' &

Step 2b: -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



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 2c: Add control points to mark white matter not inside the white matter surfaces

More on how to make these corrections is coming soon!

Step 2d: 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-cp -autorecon3 -subjid $SUBJ

… where $SUBJ is the subject identifier. NB: This is a different command than the one used in Step 1! 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 3