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Surface ROI Volume ROI• lh.OccROIs.1D.dset (created on the previous slide) can be transformed into avolume ROI with 3dSurf2Vol• Execute: source run_3dSurf2Vol3dSurf2Vol -spec../SurfData/SUMA/DemoSubj_lh.spec \-surf_A lh.smoothwm.asc \-surf_B lh.pial.asc \-sv DemoSubj_SurfVol_Alnd_Exp+orig \-grid_parent DemoSubj_SurfVol_Alnd_Exp+orig \-map_func max \-f_steps 10 \-f_p1_mm -0.5 -f_pn_fr 0.5 \-sdata lh.OccROIs.niml.dset \-prefix lh.OccROIs-grid_parent specifies the output volume’s geometric properties-f_p1_mm, -f_pn_fr: Specify extensions on node pair segment, either in mm orfractions of segment length (both used simultaneously here for illustration)-sdata_1D: Specify surface data fileHands-On29 Oct 2009 SSCC/NIMH 80
Surface ROI Volume ROI• Mention also other programs for volume computations?• Selection of ROIs by name?• Plug for run_ programs….Hands-On29 Oct 2009 SSCC/NIMH 81
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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 (
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
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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: Surface ROI Volume ROI• ROIs fil
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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