FreeSurfer Troubleshooting

Manual Interventions

  1. Erase voxels
  2. Fill voxels
  3. Clone voxels (ie, copy from one volume to another)
  4. Add “Control Points”

After manual intervention, re-run parts of recon-all
Manual interventions should take less than 30min

It is also possible to re-run recon-all with different parameters which is good for systematic or large errors

Workflow in Stages

  1. recon-all -autorecon1 (Stages 1-5)
  2. Check talairach transform, skull strip, normalization
  3. recon-all -autorecon2 (Stages 6-23)
  4. Check surfaces
    1. Add control points: recon-all -autorecon2 -cp (Stages 10-23)
    2. Edit wm.mgz: recon-all -autorecon2 -wm (Stages 13-23)
    3. Edit brainmask.mgz: recon-all -autorecon2 -pial (Stage 23)
  5. recon-all -autorecon3 (Stages 24-30)

Manual Edits Applied to Volumes not Surfaces

Erase Fill Clone Control Points
brain mask X X X
T1.mgz X
wm.mgz X X

Skull Strip Error: Too Much Removed

  • Use “clone” tool to manually correct, or adjust watershed parameters and run 
  • default watershed is 25, higher means strip less)
  • recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatlas -s <subj>
  • recon-all -s <subject> -autorecon2 -autorecon3

Skull Strip Error: Not Enough Removed

  • Eye Socket classified as WM due to Skull Strip Failure
  • Erase in wm.mgz then run:
  • recon-all -s <subject> -autorecon2-wm -autorecon3
  • Dura and GM have extremely similar intensity characteristics on most T1-weighted sequences (but different T2*!)
  • Typical fix: edit the brainmask.mgz to erase dura/blood vessels, and run
  • recon-all -s <subject> -autorecon-pial

Segmentation Errors

  • White matter classified as non-White Matter
  • Gray Matter classified as White-Matter
  • Causes:
    • Intensity Normalization Failures
    • Partial voluming
  • Fill in wm.mgz then run:
  • recon-all -s <subject> -autorun2-wm -autorecon3

Intensity Normalization

  • Removes B1 bias field
  • NU (MRI) nu.mgz
  • Presegmentation (T1.mgz)
    • Most WM = 110 intensity
    • Pre- and Post-Skull Strip
  • Intensity Normalization Failure: Most WM in T1 volume (T1.mgz) should be close 110.
  • Can fix by editing wm.mgz or adding “Control Points” (+). 
  • Beware partial voluming
  • recon-all -s <subject> -autorecon2 -autorecon3

Control Points

  • Used to rescale intensity near the control point
  • Must go in voxels that are fully WM but not 110 !!!
  • Use sparingly
  • Not associated with a partial volume
  • Can be created viewing any volume
  • Saved in a separate text file (eg, bert/tmp/control.dat)

Segmentation Errors: Topological Defects

  • Hole: Partial Voluming: WM+GM looks like non-WM, it is segmented as non-WM and creates a hole
  • Handle: Something bright in a sulcus that gets classified as WM. Does not happen often.
  • These get automatically fixed, usually correctly, but not always.
  • Holes: fill voxels in the wm.mgz
  • Handles: erase voxels in teh wm.mgz

FreeSurfer Remembers!

  • When manual edits are made, the changes are saved in a way that indicates manual changes were made
  • Re-running with a new version preserves these changes.


  • Hard Errors (recon-all.log file)
  • Soft Errors -surfaces not accurate
  • Change volumes, regenerate surfaces
  • Manual touch ups (erase, fill, clone, control points)
  • Volumes: brainmask.mgz, wm.mgz, T1.mgz
  • Skull strip: too much, not enough
  • Segmentation: WM Classified as non-WM, or reverse
  • FreeSurfer keeps track of edits
  • Look at all 3 views
  • Use tkregster2 to fix incorrect talairach.xfm
  • Shold take less than 30min (or even 15min)
  • If you don’t know, leave it alone