cortical reconstruction with freesurfer surfer.nmr.mgh.harvard.edu greve/surferfest3.ppt douglas n....
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Cortical Reconstruction with FreeSurfer
surfer.nmr.mgh.harvard.eduwww.nmr.mgh.harvard.edu/~greve/surferfest3.ppt
Douglas N. Greve
MGH-NMR CenterHarvard University
Acknowledgements• Bruce Fischl• Anders Dale• Marty Sereno• Doug Greve• Xiao Han• Nick Schmansky• Florent Segonne • Yasunari Tosa • CMA (Nikos Makris, Dave Kennedy)• Jenni Pacheco, Brian Quinn, Rahul
Desikan, Ron Killiany, …
Outline• What you can get from FreeSurfer• Surface Reconstruction Theory• Surface Reconstruction with FreeSurfer• Demo• Tutorial• Stuff not covered:
• Mapping functional data to the surface• Surface-based group analysis
Administratia• surfer.nmr.mgh.harvard.edu/fswiki • Platforms: Linux and Mac• Registration• Versions – stable vs dev• FreeSurfer mailing list• Important! How to report a bug!
• Version• Command-line• Error description• subjid/scripts/reconall.log• [email protected]
What FreeSurfer Can Do for You
• “Models” of cortical surfaces
• Morphological measures of cortex
• Surfaced-based registration to atlas
• Automatic surface labeling/segmentation
• Automatic volume labeling/segmentation
• Surface-based group analysis
• Visualization in the volume and surface
Surface Model
• Mesh (“Finite Element”)
• Vertex = point of 6 triangles
• XYZ at each vertex
• Triangles/Faces ~ 150,000
• Area, Distance
• Curvature, Thickness
• Moveable
Cortical Morphometry
Thickness
Sulcal Curvature
Gyrus
“Mean” CorticalSurface+
-Pial
White/Gray
Sulcus
Inter-Subject AveragingS
ubje
ct 1
Sub
ject
2
Native Spherical Spherical
Surface-to- Surface
Surface-to- Surface
GLM
Demographics
mris_glm
Automatic Volume Labeling
• Subcortical Segmentation
• Caudate• Putamen• Pallidum• Hippocampus• Amygdala• Nucleus Acumbens• Ventricles • White Matter• Cerebellum• …
Surface Reconstruction Theory• Find white/gray surface
• Find pial surface
• “Find” = create mesh– Vertices, neighbors, triangles, coordinates
– Accurately follows boundaries between tissue types
– “Topologically Correct”
• closed surface, no donut holes
• no self-intersections
– Subcortical Segmentation along the way
Find “Subcortical Mass”
• All White Matter
• All Subcortical Structures
• Ventricles
• Excludes brain stem and cerebellum
• Hemispheres separated
• Connected (no islands)
• Many Stages … More Later …
Tessellation and Topology Fixing
• Mosaic of triangles (“tessellation”)
• Donut holes, handles
• Automatic topology fixer
orig surface surf/lh.orig surf/rh.orig
White Matter Surface• Nudge orig surface
• Follow T1 intensity gradients
• Smoothness constraint
• Vertex Identity Stays
Details on Getting the Subcortical Mass
• Hardest part
• Some FreeSurfer background
• All Stages of Processing
• Volumetric Processing
FreeSurfer Directory Tree
bert
bem label morph mri scripts surf tiff
orig T1 brain aseg wm filled
Subject ID
mksubjdirs SubjectId
Each data set has its own unique SubjectId (eg, bert)
mksubjdirs bert
Exercise A:https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion
Individual StagesVolumetric Processing Stages (subjid/mri):1. Motion Cor, Avg, Conform (orig.mgz)2. Talairach transform computation3. Non-uniform inorm (nu.mgz)4. Intensity Normalization 1 (T1.mgz)5. Skull Strip (brain.mgz)
6. EM Register (linear volumetric registration) 7. CA Intensity Normalization 8. CA Non-linear Volumetric Registration 9. CA Label (Volumetric Labeling) (aseg.mgz)
10. Intensity Normalization 2 (T1.mgz)11. White matter segmentation (wm.mgz)12. Edit WM With ASeg13. Fill and cut (filled.mgz)
Surface Processing Stages (subjid/surf):14. Tessellate (?h.orig)15. Smooth1 (?h.smoothwm)16. Inflate1 (?h.inflated)17. QSphere (?h.qsqhere)18. Automatic Topology Fixer (?h.orig)19. Euler Number20. Smooth221. Inflate222. Final Surfs (?h.white,?h.pial)23. Cortical Ribbon Mask
24. Spherical Morph25. Spherical Registration 26. Spherical Registration27. Map average curvature to subject28. Cortical Parcellation (Labeling)29. Cortical Parcellation Statistics30. Cortical Parcellation mapped to ASeg
recon-all -help Note: ?h.orig means lh.orig or rh.orig
Green = Manual Intervention?
Motion Correction and Averaging
001.mgz
002.mgz
+ rawavg.mgz
orig
001.mgz 002.mgz
mri
rawavg.mgzDoes not change native resolution.
Conform
rawavg.mgz
orig.mgz
mri
rawavg.mgz
Changes to 256^3, 1mm^3All volumes will be conformed.
orig.mgz
Talairach Transform
• Computes 12 DOF transform matrix
• Does NOT resample
• MNI305 template
• Used to help find structures (eg, CC)
• Can also be used to localize functional activation
• mri/transforms/talairach.xfm
mri
transforms
talairach.xfm
Intensity Normalization
• Removes B1 bias field
• NU (MNI) nu.mgz
• Presegmentation (T1.mgz)– All WM = 110 intensity– Pre- and Post-Skull Strip
T1 Volume
Automatic Volume Labeling
• Used to fill in subcortical structures for creating subcortical mass• Usefull in its own right• aseg.mgz
ASeg Volume
White Matter Segmentation• Separates white matter from everything else
• “Fills in” subcortical structures
• Cerebellum removed, brain stem still there
• Somewhat redundant with aseg
• wm.mgz
WM Volume
Fill and Cut (Subcortical Mass)• Fills in any voids• Removes any islands• Removes brain stem• Separates hemispheres (each hemi has different value) • filled.mgz – “Subcortical Mass”
WM Volume Filled Volume
Pressing the Buttons
• Creating a FreeSurfer subject directory• Adding your data• The SUBJECTS_DIR environment variable• Automatic reconstruction• Actual Reconstruction and Troubleshooting• Downloading and Installing• Getting Help• Tutorial Overview
FreeSurfer Directory Tree
bert
bem label morph mri scripts surf tiff label
orig T1 brain wm aseg
Subject ID
mksubjdirs SubjectId
Each data set has its own unique SubjectId (eg, bert)
mksubjdirs bert
Exercise A:https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion
Add Your Data• mri_convert yourdicom.dcm bert/mri/orig/001.mgz• mri_convert yourdicom.dcm bert/mri/orig/002.mgz• …
bert
bem label morph mri scripts surf tiff label
orig
001.mgz 002.mgz
Exercise A:https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion
MGZ – Compressed MGH Format
Automatic Reconstruction
Come back in 48 hours …
Check your results – do the white and pial surfaces follow the boundaries?
-- Not normally how we proceed …
recon-all –s bert –autorecon-all
Partial Voluming –WM classified as Non-WMin thin strands in Temporal Lobe
Exercise F:https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FixingDefects
Eye Socket classified as WM.Skull Strip Failure.
Exercise F:https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FixingDefects
Exercise F:https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FixingDefects
“Hypo-Intensities”White Matter Lesions
Blood VesselWhite/Gray OK, butPial Inaccurate
Exercise G:https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits
Exercise C:https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints
Intensity Normalization Failure. All WM in T1 volume (T1.mgz) should be 110.Can fix by adding “Control Points”. Beware partial voluming!
Exercise D:https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripTutorial
Skull Strip Failure
Individual StagesVolumetric Processing Stages (subjid/mri):1. Motion Correct and Average (orig.mgz)2. Talairach transform computation3. Non-uniform inorm (nu.mgz)4. Intensity Normalization 1 (T1.mgz)5. Skull Strip (brain.mgz)
6. EM Register (linear volumetric registration) 7. CA Intensity Normalization 8. CA Non-linear Volumetric Registration 9. CA Label (Volumetric Labeling) (aseg.mgz)
10. Intensity Normalization 2 (T1.mgz)11. White matter segmentation (wm.mgz)12. Edit WM With ASeg13. Fill and cut (filled.mgz)
Surface Processing Stages (subjid/surf):14. Tessellate (?h.orig)15. Smooth1 (?h.smoothwm)16. Inflate1 (?h.inflated)17. QSphere (?h.qsqhere)18. Automatic Topology Fixer (?h.orig)19. Euler Number20. Smooth221. Inflate222. Final Surfs (?h.white,?h.pial)23. Cortical Ribbon Mask
24. Spherical Morph25. Spherical Registration 26. Spherical Registration27. Map average curvature to subject28. Cortical Parcellation (Labeling)29. Cortical Parcellation Statistics30. Cortical Parcellation mapped to ASeg
recon-all -help Note: ?h.orig means lh.orig or rh.orig
Green = Manual Intervention?
Actual Workflow
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 brain.mgz: recon-all –autorecon2-pial (Stage 23)
5. recon-all –autorecon3 (Stages 24-30)
Note: all stages can be run individually
Tutorial Exerciseshttps://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ExercisesYou don’t actually have run anything!
• Exercise A: mksubjdir and convert a DICOM volume into mgz format • Exercise B: SKIP (check talairach registration)• Exercise C: Using control points for intensity normalization • Exercise D: Fixing skull stripping • Exercise E: View orig, T1, brain, and wm volumes with tkmedit• Exercise F: Recognizing and fixing inaccuracies in the white matter surfaces • Exercise G: Correcting Pial Surfaces
Administratia• surfer.nmr.mgh.harvard.edu/fswiki • Platforms: Linux and Mac• Registration• Versions – stable vs dev• FreeSurfer mailing list• Important! How to report a bug!
• Version• Command-line• Error description• subjid/scripts/reconall.log
• Stuff not covered:• Mapping functional data to the surface• Surface-based group analysis