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@SUMA_Make_Spec_* scripts• These scripts prepare surfaces and volumes for use with SUMA:★ @SUMA_Make_Spec_FS★ @SUMA_Make_Spec_SFfor FreeSurfer surfacesfor SureFit surfaces★ @SUMA_Make_Spec_Caret for Caret surfaces• Output of these scripts include:★ Surface Volume: SurfVol★ AFNI dataset created from anatomical MRI, used to create thesurfaces★ AFNI volumes of cortical and subcortical segmentations (FreeSurfer)★ ASCII versions of all surfaces (FreeSurfer)★ Surface specifications file: (*.spec)★ ASCII file defining relationships between family of surfaces.29 Oct 2009 SSCC/NIMH 10
Viewing Surfaces with SUMA• After @SUMA_Make_Spec_* scripts are run, surface models shouldbe in excellent alignment with SurfVol★ Use SUMA to verify alignment★ Scroll through the volume to make sure surfaces are accurate➥ Check especially for inferior temporal and occipital areas• Demo using FreeSurfer surfaces:Hands-On★ cd suma_demo/SurfData/SUMA➥ This is where the output of @SUMA_Make_Spec_FS resides★ afni –niml &➥ launches AFNI to allow the viewing of DemoSubj_lh.spec➥ the –niml option tells AFNI to listen to connections from SUMA★ suma –spec DemoSubj_lh.spec –sv DemoSubj_SurfVol+orig &➥ or execute the script: tcsh run_suma29 Oct 2009 SSCC/NIMH 11
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: A: Preparing surface modelsfor SUMA
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
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Playing with color plane order• D
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Drawing surface-based ROIs• Demo
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Surface ROI Volume ROI• ROIs fil
Page 71 and 72:
Surface ROI Volume ROI• Mention
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Smoothing data on surface models•
Page 75 and 76:
Smoothing geometry of surface• Su
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• afni_proc.pyProcessing Pipeline
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Auxiliary programs• To see a list
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• ScaleToMapAuxiliary programs★
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Developers:Brenna ArgallShruti Jape
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