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Talairach data display, for panache• Without creating individualized surfaces, you can display data on aTalairach-ed surface model.★ The surface models were created with FreeSurfer from the N27dataset. (Holmes, CJ et al. JCAT 1998)★ Anatomical volume and surfaces were Talairach-ed using AFNI andSUMA, respectively. (Surfaces created by Brenna Argall)• Demo: (close previous SUMA and AFNI sessions)★ cd suma_demo/afni_tlrc➥ You should find Anat+tlrc and a functional dataset in Talairach space★ afni –niml &➥ setup function as shown in the earlier slidessuma –spec ../SurfData_tlrc/SUMA/N27_lh_tlrc.spec \–sv Anat+tlrc➥ start communication with AFNI➥ map function onto surface➥ appreciate the geometric limitations of this approach➥ ignore the limitation and make cool picturesHands-On29 Oct 2009 SSCC/NIMH 86
• afni_proc.pyProcessing Pipelines★ With a couple of extra options (-spec and –sv), afni_proc.py canprocess single-subject data in the surface domain.★ This includes surface-based smoothing and regresion analysis.★ See example 8 in afni_proc.py -help★ All voxel wise programs will work with surface-based data★ Level-II (group) analysis programs are applicable to surface-basedresults.★ 3dcalc, 3dROIstats, 3dMEMA, 3dLME, 3dMVM, etc.• @RetinoProc★ Process retinotopic data, see @RetinoProc –help for detail includingtest dataHands-On29 Oct 2009 SSCC/NIMH 87
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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
Page 7 and 8:
The Process of Using SUMA PreSUMA (
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A: Preparing surface modelsfor SUMA
Page 11 and 12:
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
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: Smoothing geometry of surface• Su
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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