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SUrface MApping with AFNI• Surface mapping & viewing program tightly linked tointeractive AFNI — but SUMA is a separate program• Complements AFNI’s slice and volume renderingmodes– AFNI works with data defined over volumes– SUMA works with data defined over surfaces• Provides a framework for fast and user-customizablesurface-based analysis• Supports surface models created by:FreeSurfer http://surfer.nmr.mgh.harvard.eduSureFit/Caret http://stp.wustl.edu/resources/display.htmlBrainVoyager http://www.brainvoyager.com• Allows representation of 2D and 3D objects inprojection frame or surface coordinate space.29 Oct 2009 SSCC/NIMH 6
The Process of Using SUMA PreSUMA (setup phase): Collect, align, and average high-quality, high-resolution anatomical dataOn NIMH’s GE 3 Tesla scanners, 2-4 MPRAGE datasets do wellCorrect image non-uniformity Using AFNI’s 3dUniformize or the N3 normalization tool [J.G. Sled et al. 98]Create and correct surfaces Using FreeSurfer, SureFit, or BrainVoyager CircumSUMA: Create standard-mesh version of surface models Align surface with experimental data Using @SUMA_AlignToExperimentMap experimental volumetric data to surfaceUsing AFNI and SUMA (interactively or with command line program)Time series analysis on datasets defined over surface domain Smoothing, statistics, clustering, group analysis.29 Oct 2009 SSCC/NIMH 7
Page 1 and 2: SUMAStatistical & Scientific Comput
Page 3 and 4: 29 Oct 2009 SSCC/NIMH 3
Page 5: SUMA29 Oct 2009 SSCC/NIMH 5
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 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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