Alignment and Atlases

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-72-Mutual Information• Entropy of 2D histogram H({r ij }) = –Σ ij r ij log 2 (r ij ) Number of bits needed to encode value pairs (i,j)• Mutual Information between two distributions Marginal (1D) histograms {p i } <strong>and</strong> {q j } MI = H({p i }) + H({q j }) - H({r ij }) Number of bits required to encode 2 values separately minus number of bitsrequired to encode them together (as a pair) If 2D histogram is independent (r ij = p i ⋅q j ) then MI = 0 = no gain from joint encoding• 3dAllineate minimizes E[J,I] = –MI(J,I) with -cost mi
-73-Normalized MI• NMI = H({r ij }) ⁄ [ H({p i }) + H({q j }) ] Ratio of number of bits to encode value pair divided by number of bits to encode twovalues separately Minimize NMI with -cost nmi• Some say NMI is more robust for registration than MI, since MI can be large when thereis no overlap between the two images NOoverlapBADoverlap100%overlap
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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
Page 21 and 22: -21-ATLAS DEFINITIONSTemplate Space
Page 23 and 24: -23-Registration To Standard Spaces
Page 25 and 26: -25-• Hidden in GUI - right click
Page 27 and 28: -27-• Stage 2: Scaling to Talaira
Page 29 and 30: -29-Automatic Talairach Transformat
Page 31 and 32: -31-Templates included with AFNITT_
Page 33 and 34: -33-Applying a transform to followe
Page 35 and 36: -35-@auto_tlrc Results are Comparab
Page 37 and 38: -37-Atlas/Template Spaces Differ In
Page 39 and 40: -39-From Space To SpaceTLRCMNIMNI-A
Page 41 and 42: -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 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 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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