Alignment and Atlases

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-98-• Class example - Writing anat (Underlay) datasets to disk: You can use [Define Datamode] ⇒ Write ⇒ [ULay] to write the currentanatomical dataset .BRIK out at the current grid spacing (cubical voxels), usingthe current anatomical interpolation mode After that, [View ULay Data Brick] will become available➥ ls ⇒ to view newly created .BRIK files in the demo_tlrc/ directory:anat+acpc.HEAD anat+acpc.BRIKanat+tlrc.HEAD anat+tlrc.BRIK• Class example - Writing func (Overlay) datasets to disk: You can use [Define Datamode] ⇒ Write ⇒ [OLay] to write the currentfunctional dataset .HEAD and BRIK files into our demo_tlrc/ directory After that, [View OLay Data Brick] will become available➥ ls ⇒ to view newly resampled func files in our demo_tlrc/ directory:func_slim+acpc.HEADfunc_slim+acpc.BRIKfunc_slim+tlrc.HEADfunc_slim+tlrc.BRIK
-99-• Command line program adwarp can also be used to write out .BRIK files fortransformed datasets:adwarp -apar anat+tlrc -dpar func+orig The result will be: func+tlrc.HEAD and func+tlrc.BRIK• Why bother saving transformed datasets to disk anyway? Datasets without .BRIK files are of limited use:➥ You canʼt display 2D slice images from such a dataset➥ You canʼt use such datasets to graph time series, do volume rendering,compute statistics, run any command line analysis program, run anyplugin…➭ If you plan on doing any of the above to a dataset, itʼs best to haveboth a .HEAD and .BRIK files for that dataset
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-4-Alignment tools in AFNI (continu
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-6-• Most image registration meth
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-8-• AFNI program 3dvolreg is for
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-11-Motion correction - caveats•
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-13-align_epi_anat.py• Goal: Want
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-15-Alignment Visualization in AFNI
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-17-Rat BrainsAlignmentof12hourMang
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-19-ATLASES
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-21-ATLAS DEFINITIONSTemplate Space
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-23-Registration To Standard Spaces
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-25-• Hidden in GUI - right click
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-27-• Stage 2: Scaling to Talaira
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-29-Automatic Talairach Transformat
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-31-Templates included with AFNITT_
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-33-Applying a transform to followe
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-35-@auto_tlrc Results are Comparab
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-37-Atlas/Template Spaces Differ In
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-39-From Space To SpaceTLRCMNIMNI-A
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-41-Atlases Distributed With AFNITT
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-43-Atlases Distributed With AFNI:A
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-45-[Where am I?]Shows you where yo
Page 47 and 48: -47-• whereami can report on the
Page 49 and 50: -49-The Future …• New atlases -
Page 51 and 52: -51-Neighborhoods in Space -Transfo
Page 53 and 54: -53-• Histogram cartoons:IIIJJJ
Page 55 and 56: -55-• grayscale underlay = J(x) =
Page 57 and 58: -57-• The future for 3dAllineate:
Page 59 and 60: -59-Appendix AInter-subject, inter-
Page 61 and 62: -61-• Anatomical coverage differs
Page 63 and 64: -63- Solutions to these problems:
Page 65 and 66: -65- Recipe above does not address
Page 67 and 68: -67-
Page 69 and 70: -69-Algorithmic Features• Goal is
Page 72 and 73: -72-Mutual Information• Entropy o
Page 74 and 75: -74-Hellinger Metric• MI can be t
Page 76 and 77: -76-3dAllineateʼs Symmetrical CR
Page 78 and 79: -78-Test: Monkey EPI - Anat6 DOFHEL
Page 80 and 81: -80-Test: Monkey EPI - Anat11 DOFHE
Page 82 and 83: -82-• Listen up folks, IMPORTANT
Page 84 and 85: -84- First goal is to mark top midd
Page 86 and 87: -86-• AC-PC Markers Cheat Sheet T
Page 88 and 89: -88-Notes on positioning AC/PC mark
Page 90 and 91: -90-• Scaling to Talairach-Tourno
Page 92 and 93: -92-Using the same methods as befor
Page 94 and 95: -94-• Automatic creation of “fo
Page 96 and 97: -96-“Warp on demand” viewing of
Page 100 and 101: -100- Examination of time series fr
Page 102 and 103: -102-Real-Time 3D Image Registratio
Page 104: -104-• Screen capture fromexample
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