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Using Standard-Mesh Surfaces• Subsequent analysis will use standard-mesh surfaces, not originals★ Map single-subject data to corresponding standard-mesh surfaces.★ Use any of AFNI’s 3dXXX voxel-based statistical tools to perform withinandcross-subject analysis in the surface domain★ 3dXXX programs can read/write NIML-formatted datasets defined oversurface domains as well as true 3D volume files• Creating standard-mesh surfaces takes a couple of minutes per subject• You can compare original and standard surfaces using:– SUMA• create a spec file containing both original and standard-meshsurfaces.• open two views, one showing original surface and one showingstandard-mesh surfaces• link viewers by coordinates (not by node index) from the SUMAcontroller (ctrl+u)– CompareSurfaces Written by Shruti Japee• a program that calculates the distance from each node on surface 1along its normal to surface 2– SurfaceMetrics• a program that calculates metrics of the mesh like edge lengths,triangle areas, curvature, etc.29 Oct 2009 SSCC/NIMH 40
Artifacts with standard meshes• In the past, there have been localized distortions between thestandard-mesh surface and the original surface.• These had all been caused by topological errors in the originalspherical surfaces.• SurfQual was written to highlight these errors★ if causing distortions, errors must be fixed with the program used togenerate them.★ These topological errors can be ignored if they do not cause any visibledistortions in the standard-mesh surfaces.• Distortions in triangle sizes are the dual of compression/stretchingon the registered sphere. If distortions are extreme, revisitregularization parameters of the registration procedure.29 Oct 2009 SSCC/NIMH 41
Page 1 and 2: SUMAStatistical & Scientific Comput
Page 3 and 4: 29 Oct 2009 SSCC/NIMH 3
Page 5 and 6: SUMA29 Oct 2009 SSCC/NIMH 5
Page 7 and 8: The Process of Using SUMA PreSUMA (
Page 9 and 10: A: Preparing surface modelsfor SUMA
Page 11 and 12: Viewing Surfaces with SUMA• After
Page 13 and 14: Check for proper alignment and defe
Page 15 and 16: Basic SUMA viewer functions• Pryi
Page 17 and 18: Basic SUMA viewer functions• Pick
Page 19 and 20: Recording your beautiful SUMA image
Page 21 and 22: What’s a surface made of?NodeEdge
Page 23 and 24: • Geometry: Spatial location★ X
Page 25 and 26: Viewing the group of surfaces• Sw
Page 27 and 28: Standardizing Surfaces For Group An
Page 29 and 30: Subject dataSpherical WarpingYellow
Page 31 and 32: Our WayInstead of interpolatingdata
Page 33 and 34: Standard meshes for 6 subjects• 6
Page 35: Creating Standard-Mesh Surfaces•
Page 39 and 40: B: Aligning Surface w/ Experiment D
Page 41 and 42: • Launch AFNI to check that volum
Page 43 and 44: Mapping Options• Surface/volume I
Page 45 and 46: Mapping Habits• When mapping data
Page 47 and 48: Command-line Mapping• 3dVol2Surf
Page 49 and 50: Format of surface-based datasets•
Page 51 and 52: • Demo (continued):Graphing Time
Page 53 and 54: • Demo (continued):• Mapping Pa
Page 55 and 56: • Demo (continued):• The Colorm
Page 57 and 58: • Demo (continued):• Interactiv
Page 59 and 60: • Demo (Continued):• Dset Info
Page 61 and 62: Color overlay planes• Colorized D
Page 63 and 64: Layering fore- & background planes
Page 65 and 66: Playing with color plane order• D
Page 67 and 68: Drawing surface-based ROIs• Demo
Page 69 and 70: Surface ROI Volume ROI• ROIs fil
Page 71 and 72: Surface ROI Volume ROI• Mention
Page 73 and 74: Smoothing data on surface models•
Page 75 and 76: Smoothing geometry of surface• Su
Page 77 and 78: • afni_proc.pyProcessing Pipeline
Page 79 and 80: Auxiliary programs• To see a list
Page 81 and 82: • ScaleToMapAuxiliary programs★
Page 83: Developers:Brenna ArgallShruti Jape

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