Alignment and Atlases

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-94-• Automatic creation of “follower datasets”: After the anatomical +orig dataset in a directory is resampled to +acpc and+tlrc coordinates, all the other datasets in that directory will automatically gettransformed datasets as well➥➥These datasets are created automatically inside the interactive AFNI program,and are not written (saved) to disk (i.e., only header info exists at this point)How followers are created (arrows show geometrical relationships): anat+orig → anat+acpc → anat+tlrc ↑ ↓ ↓ func+orig func+acpc func+tlrc
-95- How does AFNI actually create these follower datsets?➥ After [Transform Data] creates anat+acpc, other datasets in the samedirectory are scanned➭ AFNI defines the geometrical transformation (“warp”) from func_slim+origusing the to3d-defined relationship between func_slim+orig and anat+orig, AND the markers-defined relationship between anat+orig and anat+acpc • A similar process applies for warping func_slim+tlrc➭ These warped functional datasets can be viewed in the AFNI interface:Functional dataset warped toanat underlay coordinatesfunc_slim+orig “func_slim+acpc” “func_slim+tlrc” Next time you run AFNI, the followers will automatically be created internally againwhen the program starts
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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
Page 43 and 44: -43-Atlases Distributed With AFNI:A
Page 45 and 46: -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 96 and 97: -96-“Warp on demand” viewing of
Page 98 and 99: -98-• Class example - Writing ana
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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Alignment and Atlases

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