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Drawing surface-based ROIs• Demo (Continued)★ To fill a closed loop, click inside the loop.➥ Note: If you have patterns that make a figure 8 jealous you mighthave to do multiple fills.★ Press Finish when you are done drawing and have set the drawinglabel and value to your liking.★ Now you can draw another ROI, and another and another.★ Drawing can be started/continued on any of the related surfaces➥ When you hit ‘Join’, the loop is closed using the surface where theROI was created★ Switch ROI to switch between ROIs and delete/modify them.★ Load to load ROIs from file★ Save to save ROIs to file➥ 1D or NIML = Format of ROI file➥ This or All = which ROI to save into the fileHands-On29 Oct 2009 SSCC/NIMH 78
Surface ROI Volume ROI• ROIs files should be transformed to dataset files (Dset).★ A dataset file has an equal number of values for each node★ You can draw two ROIs, such that some nodes belong tomore than one ROI (i.e., they have more than one value)• The program ROI2dataset is used to change ROIs to datasets• Execute: tcsh run_ROI2datasetROI2dataset -label_dset lh.OccROIs.niml.dset \-input lh.OccROIs.niml.roi• Note the warning:Warning SUMA_ROIv2dataset:155/2536 nodes had duplicate entries.(ie same node part of more than 1 ROI)Duplicate entries were eliminated.★ At the moment, duplicate entries are ignored, 1 st come, 1 stadopted. More options could be added if truly necessary.Hands-On29 Oct 2009 SSCC/NIMH 79
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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
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The Process of Using SUMA PreSUMA (
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A: Preparing surface modelsfor SUMA
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Viewing Surfaces with SUMA• After
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Check for proper alignment and defe
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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: Drawing surface-based ROIs• Demo
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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