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FreeSurfer Hands-On Workshop by Peggy Christidis

Join us on November 18, 2004, at the National Institutes of Health to learn FreeSurfer techniques. Create surfaces and overlay functional data using SUMA. Detailed agenda covers volume preprocessing, segmentation, and more.

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FreeSurfer Hands-On Workshop by Peggy Christidis

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  1. FREESURFER HANDS-ON WORKSHOP Peggy Christidis November 18, 2004 National Institutes of Health

  2. GOAL OF WORKSHOP Learn to create surfaces using FreeSurfer • Start with several anatomical scans (MPRAGE) • Create surface using FreeSurfer • Overlay functional data on surface using SUMA (Hands-On class for SUMA on 11-19-04)

  3. Agenda • FreeSurfer Overview • Hands-On • Volume Preprocessing • Segmentation • Tessellation/Inflation • Manual Editing/Re-inflation • Lunch Break • Hands-Off • Fix Topology • Final Surface • Cut and Flatten

  4. FreeSurfer Flowchart Volume Preprocessing Segmentation Tessellation Inflation Manual Editing Re-inflation Fix topology Final Surface Volume/Surface Postprocessing Cutting & Flattening

  5. Volume preprocessing Segmentation Tessellation Inflation Manual Editing Re-inflation Fix topology Final Surface Cutting & Flattening Volume/Surface postprocessing 1. Volume Preprocessing to3d BRIK • Convert I.* files to BRIK using AFNIto3d • Perform intensity normalization using AFNI3dUniformize • Register multiple volumes using AFNI 3dvolreg • Average the registered volumes using AFNI 3dMean • Convert to FreeSurfer format using FreeSurfer mri_convert I.* files 3dUniformize 3dvolreg 3dMean mri_convert COR

  6. AFTER BEFORE AFTER BEFORE 1. Volume PreprocessingIntensity normalization – critical for segmentation • Inhomogeneities in scanner fields cause gray and white matter intensities to vary as a function of their spatial location. • Removes residual non-uniformities in gray and white matter intensity values. • Increases gray and white matter contrast. • Sharpens the peaks of the two tissue classes. • Makes the intensity distribution of gray and white matter spatially uniform.

  7. Volume preprocessing Segmentation Tessellation Inflation Manual Editing Re-inflation Fix topology Final Surface Cutting & Flattening Volume/Surface postprocessing 1. Volume Preprocessing to3d BRIK • Convert I.* files to BRIK using AFNI to3d • Perform intensity normalization using AFNI 3dUniformize • Register multiple volumes using AFNI3dvolreg • Average the registered volumes using AFNI3dMean • Convert to FreeSurfer format using FreeSurfermri_convert I.* files 3dUniformize 3dvolreg 3dMean mri_convert COR

  8. Volume preprocessing Segmentation Tessellation Inflation Manual Editing Re-inflation Fix topology Final Surface Cutting & Flattening Volume/Surface postprocessing 2. Segmentation • Intensity normalization • Skull stripping • White matter labeling

  9. Volume preprocessing Segmentation Tessellation Inflation Manual Editing Re-inflation Fix topology Final Surface Cutting & Flattening Volume/Surface postprocessing 2. Segmentation • Intensity normalization • Skull stripping • White matter labeling

  10. Volume preprocessing Segmentation Tessellation Inflation Manual Editing Re-inflation Fix topology Final Surface Cutting & Flattening Volume/Surface postprocessing 2. Segmentation • Intensity normalization • Skull stripping • Shrink-wrap algorithm • Start with ellipsoidal template • Minimize brain penetration and curvature • White matter labeling Skull stripping

  11. Skull Stripping Courtesy: http://cogsci.ucsd.edu/~sereno/movies.html

  12. Volume preprocessing Segmentation Tessellation Inflation Manual Editing Re-inflation Fix topology Final Surface Cutting & Flattening Volume/Surface postprocessing 2. Segmentation • Intensity normalization • Skull stripping • White Matter labeling • Preliminary classification solely intensity based • Relabeling of mislabeled voxels based on neighborhood information • Define cutting planes • Find connected components and fill define cutting planes Connect components and fill segment

  13. Volume preprocessing Segmentation Tessellation Inflation Manual Editing Re-inflation Fix topology Final Surface Cutting & Flattening Volume/Surface postprocessing 3. Tessellation and Inflation • Surface Tessellation • Use two triangles to represent each face separating white matter voxels from other voxels • Smooth initial tessellation with a deformable surface algorithm • Surface Inflation • Retain shape and metrics while making the interior of sulcivisible Tessellate and smooth Inflate

  14. Inflation Courtesy: http://cogsci.ucsd.edu/~sereno/movies.html

  15. 5. Re-inflation Volume preprocessing Segmentation Inflation Manual Editing Re-inflation Fix topology Final Surface Cutting & Flattening Volume/Surface postprocessing 4. Manual editing • Examine surface for defects • manually reclassify voxels in the following areas: • Lateral ventricle • Fornix • Optic nerve • Basal ganglia • Other defect areas Fornix Lateral Ventricle Optic Nerve Basal Ganglia

  16. 7. Make final surface • Final gray/white boundary (white) • Final gray/csf boundary (pial) Volume preprocessing Segmentation Inflation Manual Editing Re-inflation Fix topology Final Surface Cutting & Flattening Volume/Surface postprocessing • Fix topology • Automatic defect removal algorithm that removes minor defects ensuring that the surface is topologically correct.

  17. Volume preprocessing Segmentation Inflation Manual Editing Re-inflation Fix topology Final Surface Cutting & Flattening Volume/Surface postprocessing 8. Cutting and flattening • For a full surface patch • For occipital patch

  18. Flattening of occipital patch Flattening of full surface Courtesy: http://cogsci.ucsd.edu/~sereno/movies.html

  19. Volume preprocessing Segmentation Inflation Manual Editing Re-inflation Fix topology Final Surface Cutting & Flattening Volume/Surface Postprocessing SUMA (Hands-On class 11-19-04) • Convert surfaces to ASCII format • Align surface volume to experiment volume • Overlay functional data onto surface • Create link between AFNI and SUMA • View function on volume and surface simultaneously • Visit SUMA website for details: • http://afni.nimh.nih.gov/ssc/ziad/SUMA/ SUMA AFNI

  20. FreeSurfer Links FreeSurfer Website (articles, download, docs, FAQ): http://surfer.nmr.mgh.harvard.edu Mail Archives: www.mail-archive.com/freesurfer@mail.nmr.mgh.harvard.edu

  21. Acknowledgements • Alex Clark • Bob Cox • Richard Doucette • Hauke Heekeren • Shruti Japee • Sean Marrett • Rick Reynolds • Ziad Saad

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