Manual Interventions
- Erase voxels
- Fill voxels
- Clone voxels (ie, copy from one volume to another)
- 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
- recon-all -autorecon1 (Stages 1-5)
- Check talairach transform, skull strip, normalization
- recon-all -autorecon2 (Stages 6-23)
- Check surfaces
- Add control points: recon-all -autorecon2 -cp (Stages 10-23)
- Edit wm.mgz: recon-all -autorecon2 -wm (Stages 13-23)
- Edit brainmask.mgz: recon-all -autorecon2 -pial (Stage 23)
- 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.
Summary
- 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