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Auxiliary programs• CreateIcosahedron (by B. Argall)★ Creates Icosahedral meshes of varying node counts• inspec★ Outputs information about a spec file• IsoSurface★ Creates an isosurface from a volumetric dataset• MakeColorMap★ Creates colormaps for use with AFNI• MapIcosahedron (by B. Argall)★ transforms the topology of surface models to standardmodels without distorting the geometry (tested withFreeSurfer’s spherical mapping).★ use to check for errors in topology of spherical surfaces• quickspec★ Creates a spec file for one or a set of surfaces (quick anddirty)• ROI2dataset★ Transforms ROI files into surface datasets29 Oct 2009 SSCC/NIMH 90
• ScaleToMapAuxiliary programs★ Transforms a set of node values to node colors based on chosencolor map• SurfaceMetrics★ Outputs other information about the surface such as the edge list,curvature, triangle areas (mostly for debugging use)• SurfClust★ Clustering on the surface• SurfMeasures (by R. Reynolds)★ Outputs node-based surface measures such as areas, volumes,thickness, surface normals, etc. etc.• SurfSmooth★ a program for filtering surface data and/or surface geometry• SurfPatch★ Creates surface patches from a set of nodes.• SurfQual★ Locates topological errors in spherical surfaces.29 Oct 2009 SSCC/NIMH 91
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SUMAStatistical & Scientific Comput
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29 Oct 2009 SSCC/NIMH 3
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SUMA29 Oct 2009 SSCC/NIMH 5
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The Process of Using SUMA PreSUMA (
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A: Preparing surface modelsfor SUMA
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Viewing Surfaces with SUMA• After
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Check for proper alignment and defe
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Basic SUMA viewer functions• Pryi
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Basic SUMA viewer functions• Pick
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Recording your beautiful SUMA image
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What’s a surface made of?NodeEdge
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• Geometry: Spatial location★ X
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Viewing the group of surfaces• Sw
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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 and 36: Creating Standard-Mesh Surfaces•
Page 37 and 38: Artifacts with standard meshes• I
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: Auxiliary programs• To see a list
Page 83: Developers:Brenna ArgallShruti Jape
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