introduction to freesurfer surfer.nmr.mgh.harvard.edu
TRANSCRIPT
Why FreeSurfer?
1. Anatomical analysis is not like functional analysis – it is completely stereotyped.
2. Registration to a template (e.g. MNI/Talairach) doesn’t account for individual anatomy.
3. Even if you don’t care about the anatomy, anatomical models allow functional analysis not otherwise possible.
ICBM Atlas
Why not just register to an ROI Atlas?
12 DOF(Affine)
Subject 1 Subject 2 aligned with Subject 1 (Subject 1’s Surface)
Problems with Affine (12 DOF) Registration
Surface and Volume Analysis
Cortical Reconstructionand Automatic Labeling
Inflation and FunctionalMapping
Surface FlatteningSurface-based IntersubjectAlignment and Statistics
Automatic SubcorticalGray Matter Labeling
Automatic Gyral White Matter Labeling
Talk Outline
1. Cortical (surface-based) Analysis.
2. Volume Analysis.
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Surface Reconstruction Overview
• Input: T1-weighted (MPRAGE,SPGR)• 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
• Generate surface-based cross-subject registration• Label cortical folding patterns• Subcortical Segmentation along the way
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Surface Model
• Mesh (“Finite Element”)• Vertex = point of triangles
• Neighborhood
• XYZ at each vertex
• Triangles/Faces ~ 150,000
• Area, Distance
• Curvature, Thickness
• Moveable
Surfaces: White and Pial
Cortical Thickness
white/gray surface
pial surface
lh.thickness, rh.thickness
• Distance between white and pial surfaces
• One value per vertex
A Surface-Based Coordinate System
Comparing Coordinate Systems and Brodmann Areas
Cumulative histogram (red=surface, blue=nonlinear
Talairach)
Ratio of surface accuracy to volume accuracy
Automatic Surface Segmentation
Precentral Gyrus Postcentral Gyrus
Superior Temporal GyrusBased on individual’s folding pattern
Inter-Subject AveragingS
ubje
ct 1
Sub
ject
2
Native Spherical Spherical
Surface-to- Surface
Surface-to- Surface
GLM
Demographics
mri_glmfit cf. Talairach
Borrowed from (Halgren et al., 1999)
Visualization
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Automatic Cortical Parcellation
Fine-tune based onindividual anatomy
Spherical Atlas based on Manual Parcellations (40 of them)
Map to IndividualThru Spherical Reg
Note: Similar methodology to volume labeling
More in the Anatomical ROI talk
Talk Outline
1. Cortical (surface-based) Analysis.
2. Volume Analysis.
Volume Analysis: Automatic Individualized Segmentation
Surface-based coordinate system/registration appropriate for cortex but not for thalamus, ventricular system, basal ganglia, etc…
Anatomy is extremely variable – measuring the variance and accounting for it is critical (more in the individual subject talk)!
Volumetric Segmentation (aseg)
Caudate
Pallidum
Putamen
Amygdala
Hippocampus
Lateral Ventricle
Thalamus
White Matter
Cortex
Not Shown:Nucleus AccumbensCerebellum
Summary• Why Surface-based Analysis?
– Function has surface-based organization– Visualization: Inflation/Flattening– Cortical Morphometric Measures– Inter-subject registration
• Automatically generated ROI tuned to each subject individually
Use FreeSurfer Be Happy
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FreeSurfer Directory Tree
bert
scripts surf label mri stats
orig.mgz T1.mgz brain.mgz wm.mgz aseg.mgz
•Subject•Subject Name
Each data set has its own unique SubjectId (eg, bert)
recon-all –i file.dcm –subject bert –all
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Other File Formats• Surface: Vertices, XYZ, neighbors (lh.white)• Curv: lh.curv, lh.sulc, lh.thickness• Annotation: lh.aparc.annot• Label: lh.pericalcarine.label• Unique to FreeSurfer • FreeSurfer can read/write:
• NIFTI, Analyze, MINC• FreeSurfer can read:
• DICOM, Siemens IMA, AFNI