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FreeSurfer surfer.nmr.mgh.harvard Register Download Platforms: Linux, Mac, Windows VM

FreeSurfer http://surfer.nmr.mgh.harvard.edu Register Download Platforms: Linux, Mac, Windows VM. freesurfer@nmr.mgh.harvard.edu. Analyzing the Individual Subject in FreeSurfer…. What happens? How do I do that? Now What?. Cortical Surface Reconstruction.

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  1. FreeSurferhttp://surfer.nmr.mgh.harvard.eduRegisterDownloadPlatforms: Linux, Mac, Windows VM freesurfer@nmr.mgh.harvard.edu

  2. Analyzing the Individual Subject in FreeSurfer… What happens?How do I do that?Now What?

  3. Cortical SurfaceReconstruction FreeSurfer creates computerized models of the brain from MRI data. Input: T1-weighted (MPRAGE,SPGR) 1mm3 resolution (.dcm) Output: Segmented & parcellated conformed volume (.mgz)

  4. MR Anatomy Caveats Surfaces are only as good as your scan. • Dependent on data quality • Contrast to noise • Signal to noise • Voxel resolution • MR Artifacts • MR susceptibility • MR distortions • Variations in MR tissue parameters across regions of the brain are altered in different populations

  5. Suggested Morphometry Sequences http://www.nmr.mgh.harvard.edu/~andre/

  6. MGZFile Format 001.mgz • mgz = compressed MGH file • Can store 4D (like NIFTI) • cols, rows, slices, frames • Generic: volumes and surfaces • Eg, Typical Anatomical volume: 256 x 256 x 128 x 1 • FreeSurfer can read: • DICOM, Siemens IMA, AFNI • FreeSurfer can read/write: • NIFTI, Analyze, MINC Careful with NIFTI! (has 32k limit; surfaces could be more)

  7. How to Get Started Use dicoms from scanner as input to Cortical Reconstruction command: recon-all -all -i <input> -s <subject> must do for each subject. Come back in 30 hours … Check your results – accurate to the tissue boundaries?

  8. Output of Cortical Surface Reconstruction

  9. Analyzing the Individual Subject in FreeSurfer… What happens?How do I do that?Now What?

  10. Individual Steps Volumetric Processing Stages (subjid/mri): 1. Motion Cor, Avg, Conform (orig.mgz) 2. Non-uniform inorm (nu.mgz) 3. Talairach transform computation (talairach/talairach.xfm) 4. Intensity Normalization 1 (T1.mgz) 5. Skull Strip (brainmask.mgz) 6. EM Register (linear volumetric registration) 7. CA Intensity Normalization (norm.mgz) 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 ASeg 13. Fill and cut (filled.mgz) Surface Processing Stages (subjid/surf): 14. Tessellate (?h.orig.nofix) 15. Smooth1 16. Inflate1 17. QSphere (?h.qsqhere) 18. Automatic Topology Fixer (?h.orig) 19. Final Surfs (?h.white ?h.pial ?.thickness) 20. Smooth2 (?h.smoothwm) 21. Inflate2 (?h.inflated) 22. Aseg Statistics (stats/aseg.stats) 23. Cortical Ribbon Mask (?h.ribbon.mgz) 24. Spherical Morph 25. Spherical Registration (?h.sphere.reg) 26. Map average curvature to subject 27. Cortical Parcellation (Labeling) 28. Cortical Parcellation Statistics 29. Cortical Parcellation mapped to Aseg 30. White Matter Parcellation (wmparc.mgz) Blue = Manual Intervention recon-all -help Note: ?h.orig means lh.orig or rh.orig

  11. What Happens During Cortical Surface Reconstruction? • Finds wm/gray boundary – white surface • Finds pial/CSF boundary – pial surface • Subcortical Segmentation • Cortical Parcellation • Generates surface-based cross-subject registration

  12. Reconstruction Stages recon-all is broken into three stages • autorecon1 • autorecon2 • autorecon3 these 3 stages are equivalent to -all

  13. -autorecon1 Volumetric Processing Stages (subjid/mri): 1. Motion Cor, Avg, Conform (orig.mgz) 2. Non-uniform inorm (nu.mgz) 3. Talairach transform computation (talairach/talairach.xfm) 4. Intensity Normalization 1 (T1.mgz) 5. Skull Strip (brainmask.mgz) 6. EM Register (linear volumetric registration) 7. CA Intensity Normalization (norm.mgz) 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 ASeg 13. Fill and cut (filled.mgz) Surface Processing Stages (subjid/surf): 14. Tessellate (?h.orig.nofix) 15. Smooth1 16. Inflate1 17. QSphere (?h.qsqhere) 18. Automatic Topology Fixer (?h.orig) 19. Final Surfs (?h.white ?h.pial ?.thickness) 20. Smooth2 (?h.smoothwm) 21. Inflate2 (?h.inflated) 22. Aseg Statistics (stats/aseg.stats) 23. Cortical Ribbon Mask (?h.ribbon.mgz) 24. Spherical Morph 25. Spherical Registration (?h.sphere.reg) 26. Map average curvature to subject 27. Cortical Parcellation (Labeling) 28. Cortical Parcellation Statistics 29. Cortical Parcellation mapped to Aseg 30. White Matter Parcellation (wmparc.mgz) recon-all -help

  14. -motioncor -autorecon1 mri orig rawavg.mgz 001.mgz 002.mgz Motion Correction and Averaging 001.mgz rawavg.mgz + 002.mgz Does not change native resolution. mri_motion_correct.fsl

  15. -motioncor -autorecon1 rawavg.mgz orig.mgz Conform Changesto 256^3, 1mm^3 All volumes will be conformed to “anatomical space”. orig Volume mri_convert -conform

  16. -nuintensitycor -autorecon1 Non-Uniform Intensity Correction • Uses MNI tool • Removes B1 bias field nu Volume mri_nu_correct.mni

  17. Intensity Bias • Left side of the image much brighter than right side • Worse with many coil elements • Makes gray/white segmentation difficult

  18. -talairach -autorecon1 Talairach Transform • Computes 12 DOF transform matrix • Does NOT resample • MNI305 template • Used to report Talairach coords in papers • mri/transforms/talairach.xfm mri transforms talairach.xfm talairach_avi

  19. -normalization -autorecon1 IntensityNormalization • Presegmentation (T1.mgz) • All WM = 110 intensity • Pre- and Post-Skull Strip T1 Volume mri_normalize

  20. -skullstrip -autorecon1 SkullStrip • Removes all non-brain • Skull, Eyes, Neck, Dura • brainmask.mgz Orig Volume Brainmask Volume mri_watershed

  21. FreeSurfer Directory Tree Each data set has its own unique SubjectId (eg, bert) Subject ID bert bem stats srcmriscripts surf tmp label trash orig T1 brainmaskwmaseg aparc+aseg wmparc

  22. -autorecon2 Volumetric Processing Stages (subjid/mri): 1. Motion Cor, Avg, Conform (orig.mgz) 2. Non-uniform inorm (nu.mgz) 3. Talairach transform computation (talairach/talairach.xfm) 4. Intensity Normalization 1 (T1.mgz) 5. Skull Strip (brainmask.mgz) 6. EM Register (linear volumetric registration) 7. CA Intensity Normalization (norm.mgz) 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 ASeg 13. Fill and cut (filled.mgz) Surface Processing Stages (subjid/surf): 14. Tessellate (?h.orig.nofix) 15. Smooth1 16. Inflate1 17. QSphere (?h.qsqhere) 18. Automatic Topology Fixer (?h.orig) 19. Final Surfs (?h.white ?h.pial ?.thickness) 20. Smooth2 (?h.smoothwm) 21. Inflate2 (?h.inflated) 22. Aseg Statistics (stats/aseg.stats) 23. Cortical Ribbon Mask (?h.ribbon.mgz) 24. Spherical Morph 25. Spherical Registration (?h.sphere.reg) 26. Map average curvature to subject 27. Cortical Parcellation (Labeling) 28. Cortical Parcellation Statistics 29. Cortical Parcellation mapped to Aseg 30. White Matter Parcellation (wmparc.mgz) recon-all -help Note: lh processed completely first, then rh.

  23. -subcortseg -autorecon2 Automatic Volume Labeling • Label subcortical structures and wm/gm • Determine volumes of subcortical structures • Used to fill in subcortical structures for later steps ASeg Volume Atlas: RB_all_2008-03-26 steps 6-9, 22

  24. -subcortseg -autorecon2 Volume-based Labeling Labeling isdetermined by location and intensity.

  25. Markov Random Field: Motivation What is the probability that cortical gray matter occurs inferior to hippocampus?

  26. Segmentation: MRF Preliminary Segmentation

  27. Final Segmentation Segmentation: MRF

  28. Why we use atlas + intensity + spatial location + geometric info + neighboring voxels + other info… • Problems with Affine (12 DOF) Registration • ROIs need to be individualized. Why not just register to an ROI Atlas? 12 DOF (Affine) ICBM Atlas Markov Random Field: Motivation Can’t segment on intensity alone What is the probability that cortical gray matter occurs inferior to hippocampus?

  29. Validation of Volume Labeling * Manual labeling done by Center for Morphometric Analysis (CMA) *Thanks to Drs Larry Seidman and Jill Goldstein for providing this data.

  30. -segmentation -autorecon2 wm Volume White Matter Segmentation • Separates white matter from everything else • “Fills in” subcortical structures • Cerebellum removed, brain stem still there mri_segment mri_edit_wm_with_aseg mri_pretess

  31. -fill -autorecon2 WM Volume Filled 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” mri_fill

  32. FreeSurfer Directory Tree Each data set has its own unique SubjectId (eg, bert) Subject ID bert bem stats src mriscripts surf tmp label trash orig T1 brainmask wm aseg aparc+aseg wmparc

  33. Tessellation -tessellation -autorecon2 orig surface surf/lh.orig surf/rh.orig • Mosaic of triangles (“tessellation”) • Errors: Donut holes, handles • - Subsequently fixed by the automatic topology fixer

  34. -inflate -autorecon2 Inflation: Visualization Gyri Sulci Dale and Sereno, 1993; Dale et al., Dale et al., 1999; Fischl et al., 1999; Fischl et al., 2000; Fischl et al., 2001

  35. Automatic Topology Fixer -fix -autorecon2 Fornix hippocampus optic nerve Ventricles and Caudate Cortical Defects Pallidum and Putamen • Holes • Handles • Automatically Fixed

  36. Manifold Surgery BEFORE AFTER

  37. White Matter Surface -finalsurfs -autorecon2 • Nudge orig surface • Follow T1 intensity gradients • Smoothness constraint • Vertex Identity stays constant

  38. Pial Surface -finalsurfs -autorecon2 • Nudge white surface • Follow T1 intensity gradients • Vertex Identity Stays

  39. -finalsurfs -autorecon2 Optimal Surface Placement Gray-WhiteBoundary OuterCorticalSurface

  40. Cortical Thickness pial surface • Distance between white and pial surfaces • One value per vertex • Surface-based more accurate than volume-based white/gray surface lh.thickness, rh.thickness

  41. Thickness Maps • Red regions are thinner • Yellow regions are thicker

  42. Curvature (Radial) • Circle tangent to surface at each vertex • Curvature measure is 1/radius of circle • One value per vertex • Signed (sulcus/gyrus) • Actually use gaussian curvature lh.curv, rh.curv

  43. FreeSurfer Directory Tree Each data set has its own unique SubjectId (eg, bert) Subject ID bert bem stats src mri scripts surf tmp label lh.white lh.curvlh.thicknesslh.pial

  44. -autorecon3 Volumetric Processing Stages (subjid/mri): 1. Motion Cor, Avg, Conform (orig.mgz) 2. Non-uniform inorm (nu.mgz) 3. Talairach transform computation (talairach/talairach.xfm) 4. Intensity Normalization 1 (T1.mgz) 5. Skull Strip (brainmask.mgz) 6. EM Register (linear volumetric registration) 7. CA Intensity Normalization (norm.mgz) 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 ASeg 13. Fill and cut (filled.mgz) Surface Processing Stages (subjid/surf): 14. Tessellate (?h.orig.nofix) 15. Smooth1 16. Inflate1 17. QSphere (?h.qsqhere) 18. Automatic Topology Fixer (?h.orig) 19. Final Surfs (?h.white ?h.pial ?.thickness) 20. Smooth2 (?h.smoothwm) 21. Inflate2 (?h.inflated) 22. Aseg Statistics (stats/aseg.stats) 23. Cortical Ribbon Mask (?h.ribbon.mgz) 24. Spherical Morph 25. Spherical Registration (?h.sphere.reg) 26. Map average curvature to subject 27. Cortical Parcellation (Labeling) 28. Cortical Parcellation Statistics 29. Cortical Parcellation mapped to Aseg 30. White Matter Parcellation (wmparc.mgz) recon-all -help Note: lh processed completely first, then rh.

  45. Surface-Based Spherical CoordSystem

  46. “Spherical” Registration Inflated Surface (Sulcal Map) Spherical Inflation Atlas (Target) High-Dimensional Registration to Spherical Template Template: average.curvature.filled.buckner.40.tiff Individual Subject

  47. -sphere -surfreg -autorecon3 Spherical InflationRegistration to Atlas Individual Subject Atlas (Target)

  48. -cortparc -autorecon3 Cortical Parcellation Spherical Template based on Manual Parcellation Map to Individual Thru Spherical Reg Fine-tune based on individual anatomy Atlases: curvature.buckner40filled.desikan_killiany; destrieux.simple

  49. Non-Cortical Areas of Surface Amygdala, Putamen, Hippocampus, Caudate, Ventricles, CC ?h.cortex.label

  50. The “Unknown” Label

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