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Dset Controls block• Demo (Continued):• Dim:★Dimming factor to apply to colormap before mapping the intensity (I)data. The colormap, if displayed on the right, is not visibly affected byDim but the colors mapped onto the surface are.★ For RGB Dsets (.col files), Dim is applied to the RGB colors directly.• Dsp:★ How to display node color values. Options include pseudocoloring,contouring (at discrete color levels), both, or none.• 1: (for 1 only)Hands-On★ If ON, view only the selected Dset’s colors. No mixing of colors in theforeground stack is done.★ If OFF, mix the color planes in the foreground stack.★ This option makes it easy to view one Dset’s colors at a time withouthaving to worry about color mixing, opacity, and stacking order.★ Needless to say, options such as ‘Ord:’ and ‘Opa:’ in this panel are oflittle use when this button is ON.29 Oct 2009 SSCC/NIMH 68
Color overlay planes• Colorized Dsets are organized into layered color planes★ 2 commonly used planes are:➥ Surface Convexity (usually in gray scale)➥ AFNI Function (usually in color)★ Planes are assigned to two groups➥ Background planes (like Convexity)➥ Foreground planes (like AFNI Function)★ Many other planes can be added to either group.• Color planes of the same group are mixed together:★ Planes are stacked based on their order and opacity.★ Opacity of 1 st plane in a group does not affect color mixing.★ There are 2 modes for mixing colors. See F7 key in SUMA.Plane 1: 80% opacityPlane 2: 30% opacity29 Oct 2009 SSCC/NIMH 71
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SUMAStatistical & Scientific Comput
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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 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: • Demo (Continued):• Dset Info
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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